Method to isolate mutants and to clone the complementing gene

ABSTRACT

The subject invention lies in the field of microorganism mutation and selection of the mutants. In particular, the invention is directed at obtaining metabolic mutants in a simple, direct and specific manner. In a preferred embodiment it is also possible to obtain desired mutants not comprising recombinant DNA, thereby facilitating incorporation thereof in products for human consumption or application, due to shorter legislative procedures. The method according to the invention involves random mutation and specific selection of the desired metabolic mutant. Knockout mutants wherein a gene associated with metabolism is absent or inactivated and mutants with increased or decreased DNA binding capacity are also claimed.

This is a divisional of application Ser. No. 08/981,729, filed Dec. 23, 1997 now U.S. Pat. No. 6,177,261, the diclosure of which is incorporated herein by reference which is a 371 PCT/NL96/00259, Jun. 24, 1996.

BACKGROUND OF THE INVENTION

The subject invention lies in the field of microorganism mutation and selection of the mutants. In particular the invention is directed at obtaining metabolic mutants in a simple, direct and specific manner. In a preferred embodiment it is also possible to obtain desired mutants not comprising recombinant DNA, thereby facilitating incorporation thereof in products for human consumption or application, due to shorter legislative procedures. The method according to the invention involves random mutation and specific selection of the desired metabolic mutant. The method can suitably be carried out automatically. Such a mutant can exhibit either increased or decreased metabolic activity. The specificity of the method lies in the selection conditions applied. The mutants obtained are mutated in their regulatory function with regard to a predetermined part of metabolism. Dependent on the selection conditions derepressed mutants can be isolated that will thus exhibit overexpression or mutants can be found in which particular metabolic enzymic activity is eliminated. It thus becomes possible to eliminate undesirable metabolic enzymic activity or to increase desirable metabolic activity.

The methods according to the invention can suitably be carried out on well characterised sources that are already widely used in industry. The overexpressing mutants can for example be used as major sources of enzymes producing huge amounts at low cost. The initial strain to be mutated will depend on several factors known to a person skilled in the art such as: efficient secretion of proteins, the availability of large scale production processes, experience with downstream processing of fermentation broth, extensive genetic knowledge and the assurance of using safe organisms.

In another aspect of the invention it has now also become possible to ascertain and identify specific metabolic gene regulating functions.

To date a method for preparing mutants that was industrially applicable and could be automated was a method of mutating without selection and subsequent analysis of the mutants for the aspect which was to be amended. An alternative method with selection always required an enrichment step, followed by selection on the basis of growth or non growth. This meant a large number of undesired mutants had first to be weeded out. Also the existing method resulted in a high number of mutants with an incorrect phenotype and thus exhibits low selectivity.

Some years ago Gist-Brocades developed and introduced the pluGBug marker gene free technology for Aspergillus niger. In the GIST 94/60 p 5-7 by G. Selten a description is given of a vector for Aspergillus niger comprising glucoamylase regulatory regions to achieve high expression levels of the gene it regulates. This was selected as regulatory region on the basis of the naturally high expression of glucoamylase by native Aspergillus niger. Using recombinant DNA techniques the regulatory region was fused appropriately to the gene of interest as was the selection marker Aspergillus AmdS, allowing selection of the desired transformants after transferring the expression cassette to the A. niger host. Multiple copies of the expression cassette then become randomly integrated into the A. niger genome. The enzyme produced as described in the article was phytase. Subsequently the generation of marker free transformants can be achieved. In the known system the generation of marker free recombinant strains is actually a two step process since the amdS gene can be used bidirectionally. First in a transformation round to select initial transformants possessing the offered expression cassette and subsequently in a second round by counterselecting for the final recombinant strain which has lost the amdS gene again. The amdS gene encodes an enzyme which is able to convert acetamide into ammonium and acetate. Acetamide is used as sole N-source in the transformation round. In the recombination round fluoro acetamide is used as selective N-source, with a second appropriate N source such as e.g. urea. As the product fluoroacetate is toxic for other cells the propagation will be limited to those cells which have lost the amdS gene by an internal recombination event over the DNA repeats within the expression cassette. The largest problem with the known method is the fact that the resulting strain is a recombinant strain. The desired characteristic has to be introduced by incorporation of “foreign” nucleic acid, which can lengthen the time required for and sometimes even prevent legislative approval. In addition the method is not suited for developing strains with amended metabolism. Due to the presence of enzyme cascades and multiple feedback loops the mere incorporation of a particular gene cannot always lead to the desired result. Overproduction of a particular product as encoded can be compensated for by concomitant overexpression of another product or down regulated thus annulling the effect of the incorporated gene. The incorporation of DNA will therefore often be a case of trial and error with the incorporation of the desired nucleic acid being selectable but the desired phenotype not necessarily concomitantly being achieved. Furthermore the loss of the marker gene is a spontaneous process which takes time and cannot be guaranteed to occur for all transformants comprising the nucleic acid cassette.

It is known that strain improvement in microorganisms can be achieved by modification of the organism at different levels. Improvement of gene expression at the level of transcription is mostly achieved by the use of a strong promoter, giving rise to a high level of mRNA encoding the product of interest, in combination with an increase of gene dosage of the expression cassette. Although this can lead to an increase of the product formed, this strategy can have a disadvantage in principle. Due to the presence of multiple copies of the promoter the amount of transcriptional regulator driving transcription can become limited, resulting in a reduced expression of the target gene or genes of the regulator. This has been observed in the case of Aspergillus nidulans strains carrying a large number of copies of the amdS gene (Kelly and Hynes, 1987; Andrianopoulos and Hynes, 1988) and in the case of A. nidulans strains carrying multiple copies of a heterologous gene under the alcA promoter (Gwynne et al., 1987). In the latter case an increase of the alcR gene, encoding the transcriptional regulator of the alcA gene, resulted in the increase of expression of the expression cassette (Gwynne et al., 1987; Davies, 1991). In analogy to the effects found in Aspergillus nidulans, in Aspergillus niger similar limitations were observed in using the glucoamylase (glaA) promoter, due to limitation of the transcriptional regulator driving transcription (Verdoes et al. 1993; Verdoes et al 1995; Verdoes, 1994). Cloning of the glaA regulatory gene has thusfar been hampered by lack of selection strategy.

In the case of the arabinase gene expression a clear competition for transcriptional regulator was found upon the increase of arabinase gene dosage (Flipphi et al. 1994), reflecting a limitation of a transcriptional regulator common to all three genes studied.

In addition to the abovementioned drawbacks of the state of the art isolation and determination of regulator genes has until now been extremely difficult due to the fact that most of the regulatory proteins exist in very low concentrations in the cell making it difficult to determine which substance is responsible for regulation. In addition generally the regulatory product is not an enzyme and can only be screened for by a DNA binding assay which makes it difficult to determine and isolate and is very time consuming. Thus far the strategies used to clone regulatory genes are e.g.:

by complementation, which however requires a mutant to be available,

by purification of the regulatory protein, which is extremely laborious, since the protein can only be characterised by its DNA binding properties. Some of these purifications include affinity chromatography using a bound DNA fragment as a matrix. One of the drawbacks in this type of purification is that often more than one protein binds both specifically as well as non-specifically to the fragment,

based on gene clustering wherein the regulatory gene is genomically clustered with the structural genes which are regulated by its gene product, e.g. the prn cluster, the alc cluster.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts the construction of the selection plasmid pIM130.

FIGS. 2A-2C depict a comparison of the activity levels of α-L-arabinofuranosidase, β-xylanase and β-xylosidase in wild-type (“w.t.”) A. niger N402 and mutant strain 5B (“5B”) cultured on MM containing 1.5% crude wheat arabinoxylan as a carbon source.

FIG. 3 depicts the results from experiments designed to increase endo-xylanase expression. A. niger strains transformed with pGX635 (“Pyr+control”), pDB-K(XA)(“DB-K(XA)-15”), pGW635+pIM230 (“pIM 230-26”) and pDB-K(XA)+pIM230 (“DB-K(XA)/pIM 230-21”), and over-expressing endo-xylanase, were assayed for activity in the presence of 1.4% crude arabino xylan. The xylanase A activity is shown for each transformant.

DETAILED DESCRIPTION OF THE INVENTION

We have now achieved a system that can be used for shortening the length of time required for registration of mutant microorganisms capable of overproduction of particular desirable enzymes. The system overcomes the problem of multiple random inserts of “foreign” nucleic acid and in particular of the selection marker gene. It does not even require foreign nucleic acid to achieve the desired characteristic. The resulting mutant strain will not comprise heterologous nucleic acid. In addition the system according to the invention enables specific mutation of metabolism and prevents a large deal of experimentation leading to undesired phenotypes.

The subject invention is directed at a nucleic acid cassette comprising a nucleic acid sequence encoding a bidirectional marker, said nucleic acid cassette further comprising a basic transcriptional unit operatively linked to the nucleic acid sequence encoding the bidirectional marker and said nucleic acid cassette further comprising an inducible enhancer or activator sequence linked to the basic transcription unit in such a manner that upon induction of the enhancer or activator sequence the bidirectional marker encoding nucleic acid sequence is expressed, said inducible enhancer or activator sequence being derived from a gene associated with activity of part of the metabolism, said inducible enhancer or activator sequence being derived from a gene associated with metabolism.

A basic transcription unit comprises any elements required for transcription of the gene to which the transcription is linked. It can comprise the promoter with or without enhancer sequences. The basic transcription unit must be operative in the host organism. The basic transcription unit must be located such that it is operatively linked to the bidirectional marker gene for transcription thereof to be possible. Suitable examples are well known for a number of host cells such as e.g. Aspergillus, Trichoderma, Penicillium, Fusarium, Saccharomyces, Kluyveromyces and Lactobacillus. In the Examples the basic transcription unit tGOX derived from the Aspergillus niger goxC transcription unit (Whittington et al. 1990) is illustrated in an operable embodiment of the invention.

The inducible enhancer or activator sequence is preferably normally involved in regulation of an enzyme cascade or involved in a part of metabolism involved with one or more feed back loops. In a further embodiment a nucleic acid cassette according to the invention comprises an inducible enhancer or activator sequence that is normally involved in carbon metabolism. Suitable examples of inducible enhancer or activator sequence to be used in a nucleic acid cassette according to the invention are the Upstream Activating Sequence (UAS) as comprised on any of the following fragments of nucleic acid:

a fragment originating from the promoters of the abfA, abfB and abnA genes encoding respectively arabinofuranosidase A, arabinofuranosidase B and endoarabinase,

a fragment originating from the glaA gene encoding glucoamylase,

a fragment containing the alcR binding site such as on the alcR and alcA promoter,

a fragment originating from the CUP1 gene,

a fragment originating from the PHO5 gene

a fragment originating from the GAL1, GAL7 or GAL10 genes,

a fragment originating from the xlnA gene

a fragment originating from the pgaII gene.

By way of example these fragments can be derived from the following organisms as is described in the literature:

a fragment originating from the promoters of the abfA, abfB and abnA genes encoding respectively arabinofuranosidase A, arabinofuranosidase B and endoarabinase of Aspergillus niger (Flipphi M. J. A. et al. 1994)

a fragment originating from the glaA gene encoding glucoamylase of Aspergillus niger, (Fowler T. et al 1990)

a fragment containing the alcR binding site such as on the alcR promoter of Aspergillus nidulans (Felenbok B. et al. 1994),

a fragment originating from the CUP1 gene of Saccharomyces cerevisiae (Hinnen A. et al. 1995)

a fragment originating from the PHO5 gene of Saccharomyces cerevisiae (Hinnen A. et al. 1995)

a fragment originating from the GAL1, GAL7 or GAL10 genes of Saccharomyces cerevisiae (Hinnen A. et al. 1995).

a fragment originating from the xlnA, xlnB, xlnC or xlnD genes of Aspergillus nidulans,

a fragment originating from the xlnB, xlnC or xlnD genes of Aspergillus niger (see elsewhere in this description),

a fragment originating from the xlnA or xlnD genes of Aspergillus tubigensis (de Graaff et al. 1994).

a fragment originating from the pgaII gene of Aspergillus niger (see elsewhere in this document).

In the Examples UAS of xlnA is illustrated in an operable embodiment of the invention.

A bidirectional marker is an art recognised term. It comprises a selection marker that can be used to indicate presence or absence of expression on the basis of the selection conditions used. A preferred bidirectional marker will confer selectability on the basis of lethality or extreme reduction of growth. Alternatively different colouring of colonies upon expression or lack of expression of the bidirectional marker gene is also a feasible embodiment. Suitable examples of known bidirectional markers are to be found in the group consisting of the facB, the NiaD, the AmdS, the Can1, the Ura3, the Ura4 and the PyrA genes. We hereby point out that PyrA homologues are also referred to in the literature as PyrG, Ura3, Ura4, Pyr4 and Pyr1. These genes can be found in i.a. the following organisms the facB gene in Aspergillus nidulans, the NiaD gene in Aspergillus niger, the NiaD gene in Aspergillus oryzae, the AmdS gene in Aspergillus nidulans, the Can1 gene in Schizosaccharomyces pombe, the Ura3 gene in Saccharomyces cerevisiae, the Ura4 gene in Saccharomyces pombe and the PyrA genes in Aspergillus, Trichoderma, Penicillium, Fusarium, Saccharomyces and Kluyveromyces.

Selection of facB mutants i.e. with a negative phenotype can occur on the basis of fluoro-acetate resistance. Selection for FAC B⁺ i.e. a positive phenotype can occur on acetate as a carbon source (Katz. M. E. and Hynes M. J. 1989). Selection of niaD mutants i.e. with a negative phenotype can occur on the basis of chlorate resistance. Selection for NIA D⁺ i.e. a positive phenotype can occur on nitrate as a nitrogen source (Unkles S. E. et al. 1989a and 1989b). Selection of amdS mutants i.e. with a negative phenotype can occur on the basis of fluor acetamide resistance. Selection for AMD S⁺ i.e. a positive phenotype can occur on acetamide as a nitrogen source. As most fungi do not have a gene encoding an acetamidase function AMD S is a dominant marker for such fungi. It has been used as such in Aspergillus niger, Aspergillus niger var, tubigensis, Aspergillus niger var. awamori, Aspergillus foetidus, Aspergillus oryzae, Aspergillus sydowii, Aspergillus japonicus, Aspergillus aculeatus, Penicillium species, Trichoderma species among others (Kelly and Hynes 1985 and Bailey et al. 1991). Selection of can1 mutants i.e. with a negative phenotype can occur on the basis of canavanine resistance, wherein canavanine is an arginine analogue. Selection for CAN 1⁺ i.e. a positive phenotype can occur on arginine (Ekwall K. 1991). The gene encoding orothidine 5′-P-decarboxylase is known as pyrA, pyrG or ura3. It has been found for various organisms e.g. Aspergilli, Trichoderma, Penicillium, Fusarium, Saccharomyces and Kluyveromyces. Selection of pyrA mutants i.e. with a negative phenotype, also described as pyrG or ura3 can occur on the basis of fluoro orotic acid resistance. Selection for PYR A⁺ and homologues thereof i.e. a positive phenotype can be done on the basis of uridine or uracil prototrophy. In the Examples pyrA from Aspergillus niger (Wilson et al.1988) is illustrated in an operable embodiment of the invention. Other examples are known to a person skilled in the art and can be readily found in the literature. The selection marker to be used will depend on the host organism to be mutated and other secondary considerations such as ease of selectability, reliability and cost of substrates to be used amongst others.

The nucleic acid cassette incorporated in a transformation or expression vector is also included in the scope of the invention. Also included is the application of such nucleic acid cassette or vector in transformation and selection methods. In particular in methods for producing mutants exhibiting overexpression of an enzyme involved in a predetermined part of metabolism, methods for producing mutants exhibiting reduced or inhibited expression of an enzyme involved in a predetermined part of metabolism and methods for determining and isolating regulatory genes involved in predetermined parts of metabolism.

Thus a method for preparing and selecting a mutant strain of microorganism, said mutation enhancing a predetermined part of metabolism in comparison to the non mutated strain, said method comprising

introducing into a host a nucleic acid cassette according to any of the preceding claims, said host not exhibiting the phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette,

culturing a resulting microorganism under conditions wherein the enhancer or activator sequence comprised on the nucleic acid cassette is normally active and under conditions wherein the bidirectional marker is expressed and wherein preferably expression of said bidirectional marker will lead to growth and non expression to non growth,

selecting a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene under the aforementioned culturing conditions,

subjecting the selected transformant to mutagenesis in a manner known per se,

culturing the resulting strain under conditions acceptable for a strain with a phenotype corresponding to the expression of the bidirectional marker and under conditions that in the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker and in the presence of a metabolisable substrate for the predetermined part of metabolism,

selecting a strain resulting from the cultivation step following mutagenesis that exhibits a phenotype corresponding to the expression of the bidirectional marker gene under selection conditions that for the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker falls within the scope of the invention.

In a suitable embodiment of this method

the inducible enhancer or activator sequence is the Upstream Activating Sequence (UAS) derived from the gene xlnA,

the predetermined part of the metabolism is the xylanolytic part of carbon metabolism,

the culturing step wherein the resulting microorganisms are cultivated under conditions wherein the enhancer or activator sequence is normally active and wherein the bidirectional marker is expressed comprises cultivation in the presence of inducer of UAS and absence of repressor of UAS and a metabolisable source of carbon,

the selecting of a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene occurs under the aforementioned culturing conditions,

the culturing step after mutagenesis of the selected transformant occurs under conditions acceptable for a strain with a phenotype corresponding to the expression of the bidirectional marker and under conditions that in the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker i.e. in the presence of repressor of UAS and in the presence of a metabolisable source of carbon and optionally also in the presence of inducer of UAS,

the selection of a strain resulting from the cultivation step following mutagenesis of a strain that exhibits a phenotype corresponding to the expression of the bidirectional marker gene occurs under selection conditions that for the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker.

In a further embodiment of this method

the nucleic acid cassette comprises a nucleic acid sequence encoding the bidirectional marker pyrA,

the host does not exhibit the pyrA+ phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette,

the culturing step wherein the resulting microorganisms are cultivated under conditions wherein the enhancer or activator sequence is normally active and wherein the bidirectional marker is expressed comprises cultivation under conditions wherein the enhancer or activator is normally active i.e. in the presence of inducer of the enhancer or activator and in the absence of repressor of the enhancer or activator and under conditions wherein the bidirectional marker is expressed,

the selecting of a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene occurs under the aforementioned culturing conditions,

the culturing step after mutagenesis of the selected transformant occurs under conditions acceptable for a strain with a phenotype corresponding to the expression of the bidirectional marker and under conditions that in the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker i.e. in the absence of inducer of the enhancer or activator or in the presence of repressor of the enhancer or activator and in the presence of a metabolisable substrate for the predetermined part of metabolism,

the selection of a strain resulting from the cultivation step following mutagenesis of a strain that exhibits a phenotype corresponding to the expression of the bidirectional marker gene occurs under selection conditions that for the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker i.e. in the absence of inducer of the enhancer or activator or the presence of repressor of the enhancer or activator.

Suitably the embodiments just mentioned can further be characterised by

the nucleic acid cassette comprising a nucleic acid sequence encoding the bidirectional marker pyrA,

the host not exhibiting the pyrA+ phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette,

the inducible enhancer or activator sequence being the UAS derived from the gene xlnA,

the culturing step wherein the resulting microorganisms are cultivated under conditions wherein the enhancer or activator sequence is normally active and wherein the bidirectional marker is expressed comprising cultivation under conditions wherein UAS is normally active i.e. in the presence of inducer of UAS such as xylose or xylan and in the absence of repressor of UAS i.e. absence of glucose and under conditions wherein the bidirectional marker is expressed,

the selecting of a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene occurs under the aforementioned culturing conditions,

the culturing step after mutagenesis of the selected transformant occurring under conditions acceptable for a strain with a phenotype corresponding to the expression of the bidirectional marker and under conditions that in the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker i.e. in the absence of inducer of UAS such as xylose or xylan or in the presence of repressor of UAS i.e. in the presence of glucose and in the presence of a metabolisable source of carbon,

the selection of a strain resulting from the cultivation step following mutagenesis of a strain that exhibits a phenotype corresponding to the expression of the bidirectional marker gene occurring under selection conditions that for the non mutated parent comprising the nucleic acid cassette result in non-expression of the bidirectional marker i.e. in the absence of inducer of UAS such as xylose or xylan or the presence of repressor of UAS i.e. in the presence of glucose.

In addition a method for preparing and selecting a non recombinant mutant strain of microorganism, said mutation enhancing a predetermined part of metabolism in comparison to the non mutated strain falls within the preferred scope of the invention. This method comprising carrying out the steps of the method according to the invention as described in the preceding paragraphs followed by crossing out in a manner known per se the nucleic acid of the introduced nucleic acid cassette.

As indicated previously a method for preparing and selecting a mutant strain of microorganism, said mutation inhibiting a predetermined part of the carbon metabolism in comparison to the non mutated strain, said method comprising

introducing into a host a nucleic acid cassette according to the invention as described above, said host not exhibiting the phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette and said host exhibiting activity of the type characterising the predetermined part of metabolism to be reduced or inhibited,

culturing a resulting microorganism under conditions wherein the enhancer or activator sequence of the nucleic acid cassette is normally active and wherein non expression of the bidirectional marker of the nucleic acid cassette will result in growth and detection of the resulting microorganism and wherein expression of said bidirectional marker will preferably be lethal or strongly inhibit growth,

selecting a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene under the aforementioned culturing conditions

subjecting the selected transformant to mutagenesis in a manner known per se,

culturing the strain resulting from the mutagenesis under conditions acceptable for growth of a strain with a phenotype corresponding to the non expression of the bidirectional marker and in the presence of a metabolisable substrate and under conditions that illustrate the reduced or inhibited activity of the predetermined part of metabolism in comparison to the non mutated host either with or without the nucleic acid cassette,

selecting a strain resulting from the cultivation step following mutagenesis that exhibits a phenotype corresponding to the reduced or inhibited activity of the predetermined part of the metabolism under selection conditions that illustrate the reduced or inhibited activity of the predetermined part of metabolism in comparison to the non mutated host with or without nucleic acid cassette such as a reduced zone of clearing upon growth on a substrate which serves as a substrate for the part of metabolism for which the activity is to be reduced or inhibited.

In a further embodiment of such a method

the inducible enhancer or activator sequence is the Upstream Activating Sequence (UAS) derived from the gene xlnA

the predetermined part of the metabolism is the xylanolytic part of carbon metabolism,

the culturing step wherein the resulting microorganisms are cultivated under conditions wherein the enhancer or activator sequence is normally active and wherein the bidirectional marker is expressed comprises cultivation in the absence of repressor of the UAS of the nucleic acid cassette, in the presence of a metabolisable source of carbon and preferably also in the presence of inducer of the UAS,

the selecting of a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene occurs under the aforementioned culturing conditions,

the culturing step after mutagenesis of the selected transformant occurs under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the bidirectional marker, under conditions that are unacceptable for growth and detection of a strain with a phenotype corresponding to the expression of the bidirectional marker i.e. in the presence of uridine and fluoro-orotic acid and under conditions that in the non mutated parent comprising the nucleic acid cassette result in activity of the predetermined part of the carbon metabolism i.e. in the presence of inducer of the UAS and a metabolisable carbon source and the absence of repressor of the UAS for example the presence of sorbitol or an alternative non repressing source of carbon in combination with an inducer like xylan or D-xylose,

the selection of a strain resulting from the cultivation step following mutagenesis that exhibits a phenotype corresponding to the reduced or inhibited activity of the predetermined part of the carbon metabolism occurs under selection conditions that illustrate the reduced or inhibited activity of the predetermined part of carbon metabolism in comparison to the non mutated host either with or without the nucleic acid casette such as a reduced zone of clearing upon growth on xylan.

An example of the method according to the preceding paragraph is provided, wherein

the nucleic acid cassette comprises a nucleic acid sequence encoding the bidirectional marker pyrA,

the host does not exhibit the PYRA+ phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette,

the culturing step wherein the resulting microorganisms are cultivated under conditions wherein the enhancer or activator sequence is normally active and wherein the bidirectional marker pyrA is expressed i.e. comprises cultivation in the presence of inducer of the enhancer or activator and in the absence of repressor of the enhancer or activator and under conditions wherein the bidirectional marker pyrA is expressed,

the selecting of a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene pyrA occurs under the aforementioned culturing conditions,

the culturing step after mutagenesis of the selected transformant occurs under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the bidirectional marker i.e. PYRA⁻ phenotype, under conditions that are unacceptable for growth and detection of a strain with a PYRA⁺ phenotype, such a phenotype corresponding to the expression of the bidirectional marker i.e. such conditions comprising the presence of uridine and fluoro-orotic acid and under conditions that in the non mutated parent comprising the nucleic acid cassette result in activity of the predetermined part of the metabolism i.e. in the presence of inducer of the enhancer or activator and a metabolisable substrate and the absence of repressor of the activator or enhancer or an alternative non repressing substrate in combination with an inducer.

In a preferred embodiment the method according to the preceding 2 paragraphs is a method, wherein furthermore

the nucleic acid cassette comprises a nucleic acid sequence encoding the bidirectional marker pyrA,

the host does not exhibit the PYRA+ phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette,

the inducible enhancer or activator sequence is the UAS derived from the gene xlnA

the culturing step wherein the resulting microorganisms are cultivated under conditions wherein the enhancer or activator sequence is normally active and wherein the bidirectional marker pyrA is expressed comprises cultivation under conditions wherein the UAS is normally active i.e. in the presence of inducer of the UAS such as xylose or xylan and in the absence of repressor of the UAS i.e. absence of glucose and under conditions wherein the bidirectional marker pyrA is expressed,

the selecting of a transformant that exhibits the phenotype corresponding to the expression of the bidirectional marker gene pyrA occurs under the aforementioned culturing conditions,

the culturing step after mutagenesis of the selected transformant occurs under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the bidirectional marker i.e. pyrA⁻ phenotype, under conditions that are unacceptable for growth and detection of a strain with a PYRA⁺ phenotype, such a phenotype corresponding to the expression of the bidirectional marker i.e. such conditions comprising the presence of uridine and fluoro-orotic acid and under conditions that in the non mutated parent comprising the nucleic acid cassette result in activity of the predetermined part of the carbon metabolism i.e. in the presence of inducer of the UAS and a metabolisable carbon source and the absence of repressor of the UAS for example the presence of sorbitol or an alternative non repressing source of carbon in combination with an inducer like xylan, or D-xylose,

the selection of a strain resulting from the cultivation step following mutagenesis that exhibits a phenotype corresponding to the reduced or inhibited activity of the predetermined part of the carbon metabolism occurs under selection conditions that illustrate the reduced or inhibited activity of the predetermined part of carbon metabolism in comparison to the non mutated host either with or without the nucleic acid cassette such as a reduced zone of clearing upon growth on xylan.

The methods described above can advantageously be carried out with a host characterised in that prior to introduction of the nucleic acid cassette it comprises nucleic acid corresponding at least in part to the nucleic acid sequence encoding the bidirectional marker, said correspondence being to a degree sufficient to allow homologous recombination in the chromosome of the bidirectional marker encoding nucleic acid comprised on the nucleic acid cassette. This aspect ensures the integration of the nucleic acid cassette at a predefined location.

In a further preferred embodiment the nucleic acid cassette will be incorporated in multiple copies to ensure that the mutagenesis step does not inactivate the bidirectional marker as this would result in incorrect results when detecting marker negative phenotypes and a decrease in the number of marker positive phenotypes.

In preferred embodiments of the invention a nucleic acid cassette has been constructed which can be used in a method for producing mutants exhibiting overexpression of an enzyme involved in a predetermined part of metabolism, a method for producing mutants exhibiting reduced or inhibited expression of an enzyme involved in a predetermined part of metabolism and a method for determining and isolating regulatory genes involved in predetermined parts of metabolism. In particular we illustrate the system as used for mutants in carbon metabolism. In the examples mutants with altered xylanolytic characteristics are described as well as arabinase and polygalacturonase mutants leading to mutants in the arabinolytic and pectinolytic pathways. In the examples Aspergillus is used as the strain to be mutated, however any other industrially acceptable microorganism will suffice. Examples of such organisms are Saccharomyces e.g. Saccharomyces cerevisiae, Saccharomyces pombe, Aspergillus e.g. Aspergillus nidulans, Trichoderma, Penicillium, Fusarium Kluyveromyces and Lactobacillus. Other examples will be obvious to a person skilled in the art and a number are also mentioned elsewhere in the description. An overexpressing or nulexpressing strain for a predetermined part of the metabolism can now be produced. We can also determine the identity and nucleic acid sequence of the activating regulator of an inducible enhancer or activator sequence. In particular when such activating regulator is involved in metabolism, more specifically when such activating regulator is involved in a part of metabolism with an enzyme cascade or feed back loop or multiple feed back loops. The nucleic acid sequence of such a regulatory gene can subsequently be used to enhance expression of target genes. Said target gene being a gene that is regulated by the regulatory gene. In a preferred embodiment such a target gene will have a binding site for the expression product of the regulator gene. Combination of a promoter normally associated with a target gene of the regulator with the regulatory gene in an expression cassette said promoter being operably linked to a homologous or heterologous sequence encoding a homologous or heterologous protein or peptide to be expressed can lead to an expression cassette extremely useful for expression of homologous and even heterologous proteins or peptides. The regulator encoding gene can be under control of its native promoter or any other promoter that can be expressed in the host cell of choice. The promoter can be constitutive or inducible, whatever is most desirable for the particular production process. Such a combination expression cassette falls within the scope of the invention as does a vector or a plasmid comprising such a cassette. The degree of expression is no longer restricted by the presence of too small an amount of regulator and thus the degree of expression of the gene to be expressed is much higher than in a corresponding host cell where the gene is expressed under control of the same promoter but without the additional presence of the regulator gene. Such increased expression is preferably achieved in cells of organisms normally comprising components of the part of the metabolic pathway to be influenced. Suitable host cells are filamentous fungi cells. The incorporation of a combined expression cassette of the type just described above in a host cell comprising a target gene of the regulator can lead to increased expression of the target gene or to increased expression of the target genes if multiple target genes are present. Preferably the target gene will be endogenous to the host cell. A host cell comprising the combination expression cassette falls within the scope of the invention.

In the examples the nucleic acid sequence xlnR of the regulator of the xylanolytic pathway xylR is provided. The target genes for this regulator have been found to comprise the genes xlnA, xlnB, xlnC and xlnD as well as axeA. The increase in xylanase A expression is illustrated and can serve to indicate the general applicability of the xylR action on a target gene of the xylR regulator. A number of sequences are known in the state of the art comprising the xlnA, B, C and D genes mentioned and the axeA gene and such information is readily available to a person skilled in the art and is to be considered incorporated herein. The promoters of preferred interest to be used in combination with xlnR nucleic acid can be selected from xlnA, xlnb, xlnC and xlnD. The use of the axeA promoter also forms a suitable embodiment of the invention. The promoters are known in the state of the art to the person skilled in the art and are considered to be incorporated herein. The xlnA promoter is described in de Graaff et al 1994. The xlnB promoter has been described by Kinoshita et al 1995). The xlnD promoter has been described in EP 95201707.7 and is included in the Sequence Listing in the sequence of sequence id no 8 of this document. The promoter sequences can either be readily synthesized on the basis of known sequences or be derived from organisms or vectors comprising them in standard manners known per se. Where the term promoter, enhancer or regulator is used naturally a fragment comprising the promoter, enhancer or regulator can be employed as long as the operability of such is not impaired. It is not necessary in the constructs according to the invention to merely incorporate the relevant sequence, any flanking non interfering sequences can be present. Not only is the nucleic acid sequence xlnR encoding the expression product xylR covered by the subject invention but also sequences encoding equivalent expression products and mutant expression products as well as the expression products themselves of the nucleic acid sequences according to the invention. Any application of xylR or xylR encoding sequences (=xlnR) disclosed herein is also applicable to the mutants and the nucleic acid sequences encoding such mutants and is to be considered incorporated mutatis mutandi.

Examples of suitable fungal cells to be used for expression of nucleic acid sequences and cassettes according to the invention are Aspergilli such as Aspergillus niger, Aspergillus tubigensis, Aspergillus aculeatus, Aspergillus awamori, Aspergillus oryzae, Aspergillus nidulans, Aspergillus carbonarius, Aspergillus foetidus, Aspergillus terreus, Aspergillus sydowii, Aspergillus kawachii, Aspergillus japonicus and species of the genus Trichoderma, Penicillium and Fusarium. Other cells such as plant cells are also feasible host cells and elsewhere in the description alternative host cells are also described.

Genes of particular interest for expressing using the expression cassette according to the invention or in combination with a nucleic acid sequence according to the invention are those encoding enzymes. Suitable genes for expressing are genes encoding xylanases, glucanases, oxidoreductases such as hexose oxidase, α-glucuronidase, lipase, esterase, ferulic acid esterase and proteases. These are non limiting examples of desirable expression products. A number of sequences are known in the state of the art comprising the genes mentioned and such information is readily available to the person skilled in the art and is to be considered incorporated herein. The genes can either be readily synthesized on the basis of known sequences in the literature or databases or be derived from organisms or vectors comprising them in a standard manner known per se and are considered to be knowledge readily available to the person skilled in the art not requiring further elucidation.

An expression product exhibiting 80%-100% identity with the amino acid sequence of xylR according to sequence id no. 9 or as encoded by the nucleic acid sequence of xlnR of sequence id. no. 9 (from nucleotide 948) is considered to be an equivalent expression product of the xylanase regulator (xylR) according to the invention and thus falls within the scope of the invention. The equivalent expression product should possess DNA binding activity. Preferably such DNA binding activity should be such that the expression product binds to the nucleic acid of the target gene to the same degree or better than the expression product binds with the amino acid sequence provided in sequence id no 9. The preferred target genes for determining binding activity are those encoding xylA, xylB, xylC and xylD i.e. the xlnA, xlnB, xlnC and xlnD genes.

Mutants of the xlnR gene expression product xylR and the encoding nucleic acid sequence xlnR according to sequence id no 9 at least maintaining the same degree of target binding activity are also claimed. Mutants considered to fall within the definition of equivalent expression products comprise in particular mutants with amino acid changes in comparison to the amino acid sequence of sequence id no 9. Such equivalents are considered suitable embodiments of the invention as are the nucleic acid sequences encoding them. Mutants with 1-15 amino acid substitutions are suitable and substitutions of for example 1-5 amino acids are also considered to form particularly suitable embodiments of the invention that form equivalent expression products. It is common knowledge to the person skilled in the art that substitutions of particular amino acids with other amino acids of the same type will not seriously influence the peptide activity. On the basis of hydrapathy profiles a person skilled in the art will realise which substitutions can be carried out. Replacement of hydrophobic amino acids by other hydrophobic amino acids and replacement of hydrophilic amino acids by other hydrophilic amino acids e.g. will result in an expression product that is a suitable embodiment of the invention. Such substitutions are considered to be covered by the scope of the invention under the term equivalents. Point mutations in the encoding nucleic acid sequence according to sequence id no 9 are considered to result in nucleic acid sequences that fall within the scope of the invention. Such point mutations can result in silent mutations at amino acid level or in substitution mutants as described above. Substitution mutants wherein the substitutions can be of any type are also covered by the invention. Preferably the identity of the mutant will be 85-100%, more preferably 90-100%, most preferably 95-100% in comparison to the amino acid sequence of sequence id no 9. As already claimed above amino acid sequences exhibiting 80-100% identity with the amino acid sequence of sequence id no 9 are covered by the term equivalent so that deletions and/or substitutions of up to 20% of the amino acid sequence, preferably of less than 15% and more preferably less than 10% most preferably of less than 5% of the amino acid sequence according to the invention are covered. Such a mutant may comprise the deletion and/or substitution in one or more parts of the amino acid sequence. Such a deletion and/or substitution mutant will however comprise an amino acid sequence corresponding to a Zn finger binding region and an amino acid sequence corresponding to the RRRLWW motif. Deletion mutants of 1-5 amino acids are considered to fall within the scope of the invention. Deletion mutants with larger deletions than 5 amino acids and/or with more than 5 substitutions and/or point mutations can also maintain the DNA binding activity. Such larger number of deletions and/or substitutions and/or point mutations will preferably occur in the N terminal half of the amino acid sequence and the corresponding part of the encoding nucleic acid sequence. The most important regions considered to be involved in regulation and activation are present in the C terminal half of the amino acid sequence from the zinc finger binding region and as such the deletion mutants will preferably comprise at least this portion of the amino acid sequence. Preferably no mutation will be present in the zinc finger binding region corresponding to that encoded in sequence id no 9 from nucleotides at position 1110 to 1260. If a mutation is present preferably it should not involve the spacing between the 6 cysteines coordinating the zinc and most preferably any mutation should not involve any of the 6 cysteines themselves. In addition preferably no mutation is present in the RRRLWW motif present in the amino acid sequence of sequence id no 9. A deletion may occur in one or more fragments of the amino acid sequence. Such a deletion mutant will however comprise an amino acid sequence corresponding to a Zn finger binding region and an acid sequence corresponding to the RRRLWW motif. Deletions of 1-15 amino acids, preferably of 1-10 amino acids and most preferably 1-5 amino acids are suitable embodiments to ensure equivalence.

Embodiments of equivalent nucleic acid sequences are a nucleic acid sequence which encodes an expression product having the same amino acid sequence as xylR of sequence id no. 9 or as encoded by the nucleic acid sequence of xlnR of sequence id. no. 9. A nucleic acid sequence encoding an expression product exhibiting 80%-100% identity with the amino acid sequence of xylR according to sequence id no 9 or as encoded by the nucleic acid sequence encoding xylR of sequence id no 9 is also considered to be an equivalent nucleic acid sequence of xlnR and falls within the scope of the invention. Another embodiment of an equivalent nucleic acid sequence according to the invention is a nucleic acid sequence capable of hybridising under specific minimum stringency conditions as defined in the Examples to primers or probes derived from nucleic acid sequence id no 9, said primers or probes being derived from the non zinc finger binding region and said primers or probes being at least 20 nucleotides in length. Generally suitable lengths for probes and primers are between 20-60 nucleotides, preferably 25-60. Preferably a probe or primer will be derived from the C-terminal encoding half of the sequence of id no 9 from the zinc finger binding region. A preferred embodiment of a nucleic acid sequence according to the invention will be capable of hybridising under specific conditions of at least the stringency illustrated in the examples to the nucleic acid sequence of id no 9. An equivalent nucleic acid sequence will be derivable from other organisms by e.g. PCR using primers based on the nucleic acid sequence id no 9 as defined above. An expression product of an equivalent nucleic acid sequence as just defined is also considered to fall within the scope of the invention. Vice versa a nucleic acid sequence encoding an equivalent amino acid sequence according to the invention is also considered to fall within the scope of the term equivalent nucleic acid sequence. In particular equivalent nucleic acid sequences and the expression products of such sequences derivable from filamentous fungi and plants are preferred embodiments of the invention. Preferably an equivalent nucleic acid sequence will comprise a nucleic acid sequence encoding a zinc finger binding region corresponding to that encoded in sequence id no 9 from nucleotides from position 1110 to 1260. In a preferred embodiment the equivalent nucleic acid sequence should encode the 6 cysteines coordinating the zinc. In a further embodiment the spacing between the cysteines should correspond to that of sequence id no 9.

Embodiments comprising combinations of the characteristics of the various embodiments of the equivalent nucleic acid sequences and expression products described above also fall within the scope of the invention. Mutants with mutation in the zinc finger binding domain are also claimed as these could exhibit increased DNA binding. Mutants exhibiting dereased DNA binding are also considered to fall within the scope of the invention. Such mutants may possess a mutation in the zinc finger binding domain. In particular mutants of the amino acid sequence provided in sequence id no 9 are claimed.

Fragments of the nucleic acid sequence according to sequence id no 9 of at least 15 nucleotides also fall within the scope of the subject invention. Such fragments can be used as probes or primers for detecting and isolating equivalent sequences. In particular a combination of two or more such fragments can be useful in a kit for detecting and/or isolating such equivalent sequences. Preferably a fragment will be derived from the C terminal half of the amino acid sequence of sequence id no 9. In a suitable embodiment of the kit one fragment will not comprise a part of the nucleic acid sequence forming the zinc finger domain. In the examples a suitable combination of fragments to be used as primers is illustrated. Any sequence obtainable through PCR as illustrated in the examples with these primers is considered to fall within the scope of the invention. The hybridisation conditions used in the examples provide the minimum stringency required for selectivity. More stringent conditions can be applied such as the stringent hybridisation conditions described by Sambrook et al for increased homology of the obtained sequences with the sequence id no 9. A lower salt concentration generally means more stringent conditions. Any fragment of the sequence according to sequence id no 9 being or encoding a polypeptide exhibiting the target gene binding activity of the complete sequence is also included within the scope of the invention as are equivalent nucleic acid sequences or amino acid sequences thereof, with equivalent being defined as defined above with regard to hybridisation and/or mutation and/or degeneracy of the genetic code for the complete sequence.

A vector or plasmid comprising the nucleic acid sequence encoding xylR or an equivalent sequence thereof as defined above also falls within the scope of the invention, as do a vector or plasmid comprising such a sequence and a host cell comprising such an additional sequence. A transformed host cell such as a microorganism or a plant cell carrying at least one additional copy of an encoding nucleic acid sequence according to sequence id no 9 or an equivalent thereof falls within the scope of the invention. Preferably the various embodiments are organized such that the sequence can be expressed in the vector, plasmid or host cell. The regulatory gene can comprise the complete sequence of id no 9 or merely the encoding sequence therof in combination with an alternative promoter that is operable in the host cell. Suitable examples of host cells have been provided elsewhere in the description. Suitable operable promoters for the various host cells that can be incorporated with the encoding sequence of sequence id no 9 will be clear to a person skilled in the art. In particular for the host cells explicitly mentioned in the description constitutive promoters or inducible promoters are known and available to work the invention without undue burden.

A process for production of homologous or heterologous proteins or peptides is provided, said process comprising expression of a nucleic acid sequence encoding the homologous protein or peptide in a host cell, said host cell further comprising an additional copy of a nucleic acid sequence encoding a regulatory gene such as xlnR or an equivalent thereof which is also expressed. A process as just described is preferably carried out with a combination nucleic acid expression cassette comprising the regulatory gene operably linked to a first promoter and said cassette further comprising a second promoter, said second promoter normally being associated with a target gene of the regulator, said target gene promoter being operably linked to the nucleic acid sequence encoding the homologous or even heterologous protein or peptide to be expressed. The first promoter can be the promoter natively associated with the regulator gene but may also be a promoter of choice that is operable in the host cell. The degree of expression is no longer restricted by the presence of too small an amount of regulator and thus the degree of expression of the gene to be expressed is much higher than in a corresponding host cell where the gene is expressed without the additional presence of the regulator gene. Such increased expression is preferably achieved in cells of organisms normally comprising components of the part of the metabolic pathway to be influenced. Suitable host cells are a plant cell or a microorganism. suitably the microorganism can be a fungus in particular it can be a filamentous fungus. Examples of suitable host cells have been given elsewhere in the descriportion and may be considered to be incorporated here. The incorporation of a combined expression cassette of the type just described above in a host cell comprising a target gene of the regulator can lead to increased expression of the target gene or to increased expression of the target genes if multiple target genes are present. Preferably the target gene will be native to the regulator. Preferably such a target gene will be endogenous to the host cell. In the examples the nucleic acid sequence of the regulator of the xylanolytic pathway xlnR is provided. The native target genes for this regulator have been found to comprise the genes xlnA, xlnB, xlnC and xlnD as well as axeA and as such these genes are preferred target genes. Other targets exist and are considered to be included in the term target gene. Various embodiments of the host cells according to the invention are covered in the claims. If both regulator sequence and target gene are natively present in the host cell the regulator sequence will be present in multiple copies. Such a microorganism will over express the gene regulated by the target gene promoter in comparison to the native microorganism.

Because now the sequence for the xylanase regulator is known it has become possible to knock out the xylanase regulator. The creation of a knockout host cell once the nucleic acid sequence of the gene to be knocked out Is known is standard technology. This method can be carried out analogously to that described in Berka et al (1990) and example 11 of EP 95201707.7, which is a copending European patent application of which a copy has been included upon filing the subject document and the example itself has also been copied into this document in the examples. Such a knockout renders a host cell which can be free of xylanolytic activities. A host cell free of xylanolytic activity due to knocking out the xlnR gene can be used to produce homologous or heterologous expression products of choice free of xylanolytic activity. A host cell with a knocked out xlnR gene falls within the scope of the invention. Such a host cell is preferably a plant cell or a filamentous fungus. Such a filamentous fungus is preferably an Aspergillus. Examples have been provided elsewhere in the description of numerous suitable host cells.

A host cell with a mutation in the regulator gene which can be arrived at using the selection and mutation method of the invention can be subjected to complementation with a regular active copy of the regulator gene. Such a complemented strain will subsequently express the products of any target genes that are regulated by the regulator. These target gene products will be absent in the case of the non complemented regulator negative mutant. Upon comparison of protein bands obtained in a manner known per se from both of the strains it will become apparent what target products are regulated by the regulator and subsequently the corresponding novel target genes can be determined in a manner known per se once its expression product has been determined. In this manner other target genes than those already known can be found for the xylanase regulator xylR in the instant examples.

EXAMPLES Example 1 Construction of the Plasmids Example 1.1 Construction of the Selection Plasmid pIM130

The selection plasmid pIM130 was constructed as depicted in FIG. 1. In PCR1 a fragment was generated from the plasmid pIM120 (de Graaff et al., 1994) using oligonucleotide 1 (SEQ ID NO: 1)

5′-CACAATGCATCCCCTTTATCCGCCTGCCGT-3′ (Formula 1)

and oligonucleotide A (SEQ ID NO: 2)

5′-CAATTGCGACTTGGAGGACATGATGGGCAGATGAGGG-3′ (Formula 2)

Oligonucleotide 1 was derived from the Aspergillus tubigensis xlnA promoter (de Graaff et al., 1994) positions 600-619 (SEQ ID NO: 5) to which 10 nucleotides containing a NsiI site were added. The 3′ end of oligonucleotide A was derived from the Aspergillus niger goxC transcription unit (Whittington et al., 1990) ending just before the translation initiation site (positions 708-723)(SEQ ID NO: 6). while the 5′ end was derived from the coding region of the A. niger pyrA gene (Wilson et al., 1988) (starting at the translation initiation site (positions 341 to 359. SEQ ID NO: 7).

Fragment A was generated by a PCR containing 10 μl 10*reaction buffer (100 mM Tris-HCl, pH 8.3. 500 mM KCl 15 mM MgCl₂, 0.01% gelatin), 16 μl 1.25 mM of each of the four deoxynucleotide triphosphates, 1 ng of the plasmid pIM120 DNA and 1 μg of each of the oligonucleotides 1 and A in a final volume of 100 μl. This reaction mixture was mixed and 1 μl TAQ polymerase (5 U/μl) (Life Technologies) was added. The DNA was denatured by incubation for 3 min at 92° C. followed by 25 cycli of 1 min 92° C. 1 min 48° C. and 1 min 72° C. After these 25 cycli the mixture was incubated for 5 min at 72° C. Analysis of the reaction products by agarose electrophoresis revealed a fragment of about 250 bp, which corresponds to the size expected based on the sequence of the genes.

In PCR2 a fragment was generated from the plasmid pCGW635 (Goosen et al., 1987) using oligonucleotide 2 (SEQ ID NO: 3)

5′-AGAGAGGATATCGATGTGGG-3′ (Formula 3)

and oligonucleotide B (SEQ ID NO: 4)

5′-CCCTCATCTGCCCATCATGTCCTCCAAGTCGCAATTG-3′ (Formula 4)

The 5′ end of oligonucleotide B was derived from the A. niger goxC basic transcription unit (positions 708-723, SEQ ID NO:6)(Whittington et al., 1990), while the 3′ end was derived from the coding region of the A. niger pyrA gene starting at the translation initiation site. Oligonucleotide 2 was derived from the pyrA coding region (positions 339-359, SEQ ID NO:7) and is spanning an EcoRV restriction site at position 602 (SEQ ID NO:7).

Fragment B was generated in an identical manner as fragment A except that in this case the reaction mixture contained 1 μg each of oligonucleotide 2 and B and 1 ng of plasmid pGW635 DNA. Analysis of the reaction products by agarose electrophoresis revealed a fragment of about 250 bp. which corresponds to the size expected based on the sequence of the pyrA gene.

Fragments A and B were isolated from agarose gel after electrophoresis. The fragments were cut from the agarose gel, after which they were recovered from the piece of agarose by electro-elution using ISC0 cups. Both on the large and the small container of this cup a dialysis membrane was mounted, the cup was filled with 0.005×TAE (50×TAE buffer per 1000 ml: 242.0 g Trizma base (Sigma), 7.1 ml glacial acetic acid, 100 ml 0.5 M EDTA pH 8.0) and the piece of agarose was placed in the large container of the cup. Subsequently the cup was placed in the electro-elution apparatus, with the large container in the cathode chamber containing 1*TAE and the small container at the anode chamber containing 1*TAE/3 M NaAc. The fragments were electro-eluted at 100 V during 1 h. After this period the cup was taken from the electro-elution apparatus and the buffer was removed from the large container, while from the small container the buffer was only removed from the upper part. The remaining buffer (200 μl) containing the DNA fragment was dialyzed in the cup against distilled water during 30 min. Finally the DNA was precipitated by the addition of 0.1 vol. 3 M NaAc, pH 5.6 and 2 vol. cold (−20° C.) ethanol. The DNA was collected by centrifugation (Eppendorf centrifuge) for 30 min. at 14,000×g. at 4° C. After removal of the supernatant the DNA pellet was dried using a Savant Speedvac vacuum centrifuge. The DNA was dissolved in 10 μl TE buffer (TE: 10 mM Tris/HCl pH7.2, 1 mM EDTA pH 8.0) and the concentration was determined by agarose gel electrophoresis, using lambda DNA with a known concentration as a reference and ethidiumbromide staining to detect the DNA.

Fragments A and B were fused in PCR3 which was identical to PCR1 except that in this case the reaction mixture contained 1 μg of each of the oligonucleotides 1 and 2 and approximately 50 ng of each of the fragments A and B. Analysis of the reaction products by agarose gel electrophoresis revealed a fragment of about 500 bp, which corresponds to the size expected based on the sequences of the genes.

The resulting fragment C was isolated from agarose gel as described and subsequently digested using the restriction enzymes NsiI and EcoRV. The DNA was digested for 3 h, at 37° C. in a reaction mixture composed of the following solutions; 5 μl (=0.5 μg) DNA solution; 2 μl of the appropriate 10×React buffer (Life Technologies); 10 U restriction enzyme (Life Technologies) and sterile distilled water to give a final volume of 20 μl. After digestion the DNA fragment was analysed by agarose gel electrophoresis and subsequently isolated from the gel as described.

For the final construction of pIM130 5 μg of the plasmid pGW635 was digested as described using 50 U of the restriction enzymes EcoRV and XbaI in a final volume of 500 μl. After separation of the products a 2.2 kb EcoRV/XbaI fragment (fragment D) was isolated from the agarose gel by electro-election. Analogously 1 μg vector pGEM-7Zf(+) (Promega) was prepared by digestion with the restriction enzymes NsiI/XbaI, which was after digestion electrophoresed and isolated from the agarose gel by electro-elution.

The plasmid pIM 130 was constructed by the following ligation reaction: 100 ng pGEM-7Zf(+) NsiI/XbaI fragment was mixed with 50 ng fragment C and 50 ng fragment D and 4 μl 5*ligation buffer (composition; 500 mM Tris-HCl, pH 7.6; 100 mM MgCl₂; 10 mM ATP; 10 mM dithiotreitol; 25% PEG-6000) and 1 μl (1.2 U/μl) T₄ DNA ligase (Life Technologies) was added to this mixture in a final volume of 20 μl. After incubation for 16 h at 14° C. the mixture was diluted to 100 μl with sterile water. 10 μl of the diluted mixture was used to transform E. coli DH5α competent cells, prepared as described by Sambrook et al., 1989.

Two of the resulting colonies were grown overnight in LB medium (LB medium per 1000 ml: 10 g trypticase peptone (BBL), 5 g yeast extract (BBL), 10 g NaCl, 0.5 mM Tris-HCl pH 7.5) containing 100 μg/ml ampicillin. From the cultures plasmid DNA was isolated by the alkaline lysis method as described by Maniatis et al. (1982), which was used in restriction analysis to select a clone harbouring the desired plasmid pIM130. Plasmid DNA was isolated on a large scale from 500 ml cultures E. coli DH5α containing pIM130 grown in LB medium containing 100 μg/ml ampicillin (Maniatis et al., 1982) The plasmid was purified by CsCl centrifugation, phenolyzed, ethanol precipitated and dissolved in 400 μl TE. The yield was approximately 500 μg.

Example 1.2 Construction of the Plasmid pIM135

From the plasmid pIM120 a second plasmid was constructed which contains the goxC basic transcription unit fused to the pyrA coding region and termination region. In PCR4 a fragment was generated from the plasmid pIM120 using oligonucleotide 3, 5′-CACAATGCATCGTATAAGTAACCTCGTTCG-3′ (Formula 5) (SEQ ID NO:10) which was derived from the goxC basic transcriptional unit (positions 640-660, SEQ ID NO:6) to which 10 nucleotides containing a NsiI site were added, and oligonucleotide 2 (Formula 3). The fragment generated was isolated from gel, digested with NsiI and EcoRV and cloned together with the 2.2 kb EcoRV/XbaI fragment of pGW635 in the plasmid pGEM-7Zf(+), which was digested with XbaI/NsiI, as described in Example 1.1., resulting in the plasmid pIM135.

The plasmid pIM135 can be used as construction vehicle for preparing vectors according to the invention with any desirable inducible enhancer or activator sequence, a UAS of a gene involved in metabolism. pIM135 comprises a basic transcription unit (tGOX) operatively linked to a bidirectional marker gene (pyrA).

Example 2 Transformation of A. niger Using the Plasmid pIM130

250 ml of culture medium, which consists of Aspergillus minimal medium (MM)(contains per liter: 6.0 g NaNO₃, 1.5 g KH₂PO₄, 0.5 g MgSO₄.7H₂O. 0.5 g KCl. Carbon source as indicated, pH 6.0 and 1 ml Vishniac solution contains per liter 10 g EDTA, 4.4 g ZnSO₄.7H₂O. 1.0 g MnCl₂.4H₂O. 0.32 g CoCl₂.6H₂O. 0.32 g CuSO₄.5H₂O. 0.22 g (NH₄)₆Mo₇O₂₄.4H₂O. 1.47 g CaCl₂.2H₂O. 1.0 g FeSO₄.7H₂O. pH 4.0) supplemented with 2% glucose, 0.5% Yeast Extract, 0.2% Casamino acids (Vitamin free), 10 mM L-arginin, 10 μM nicotinamide, 10 mM uridine, was inoculated with 1*10⁶ spores per ml of strain NW205 (cspA1, pyrA6, nicA1, argB13) and mycelium was grown for 16-18 hours at 30° C. and 250 rpm in a orbital New Brunswick shaker. The mycelium was harvested on Myracloth (nylon gauze) using a Büchner funnel and mild suction and was washed several times with SP6 (SP6: 0.8% NaCl, 10 mM Na-phosphate buffer pH 6.0). 150 mg Novozyme 234 was dissolved in 20 ml SMC (SMC: 1.33 M Sorbitol, 50 mM CaCl₂, 20 mM MES buffer, pH 5.8) to which 1 g (wet weight) mycelium was added and which was carefully resuspended. This suspension was incubated gently shaking for 1-2 hours at 30° C. every 30 minutes the mycelium was carefully resuspended and a sample was taken to monitor protoplast formation using a haemocytometer to count the protoplasts. When sufficient protoplasts were present (more then 1*10⁸) these were carefully resuspended and the mycelial debris was removed by filtration over a sterile glasswool plug. The protoplasts were collected by 10 minutes centrifugation at 3000 rpm and 4° C. in a bench centrifuge and were carefully resuspended in 5 ml STC (STC: 1.33 M Sorbitol, 50 mM CaCl₂, 10 mM Tris/HCl, pH 7.5). This wash step was repeated twice and the protoplasts were finally resuspended in STC at a density of 1*10⁸ per ml.

The transformation was performed by adding 1 μg of pIM130 DNA (dissolved in a 10-20 μl TE to 200 μl of protoplast suspension together with 50 μl of PEG buffer (PEG Buffer: 25% PEG-6000, 50 mM CaCl₂, 10 mM Tris/HCl pH 7.2), mixed gently by pipetting up and down a few times, and incubated at room temperature for 20 minutes. After this period 2 ml PEG buffer was added, the solution was mixed gently and incubated at room temperature for another 5 minutes and subsequently 4 ml of STC was added and mixed gently on a vortex mixer. This was also done using 5 μg pIM130 and 1 and 5 μg of plasmid pGW635 DNA. As a negative control 20 μl of TE was added to the protoplasts.

One ml portions of this suspension were then added to 4 ml of osmotically stabilised top agar and poured on plates (swirl gently to cover plate with top agar) containing MMS having either 100 mM D-glucose or 100 mM D-xylose as a carbon source. These media (MMS) were osmotically stabilised using 0.8 M KCL or by using 1.33 M Sorbitol.

To determine the percentage regeneration serial dilutions of the protoplasts were prepared before transformation (untreated protoplasts, kept on ice) and after transformation (obtained from the negative control). 100 μl of the 10⁻³, 10⁻⁴, 10⁻⁵ and 10⁻⁶ dilutions were plated in duplicate on 10 mM uridine supplemented MMS plates.

For the positive control, in which the fungus was transformed using the plasmid pGW635, colonies were found on all plates. However, the transformation frequency was much lower (1-10 transformants per μg plasmid DNA) on KCl stabilised medium than on sorbitol stabilised medium (100-1000 transformants per μg plasmid DNA). This was due to the much higher regeneration frequency on the latter medium, which was about 90% in comparison to 2-5% on the KCl stabilised medium.

In case of the transformations using the plasmid pIM130 transformants were found on the medium containing D-xylose as a carbon source but not on medium containing D-glucose. The frequency on sorbitol stabilised medium was about 100 per μg of plasmid DNA while the frequency on the KCl stabilised medium was less than one per μg of DNA.

Example 3 Analysis of Transformants

The transformants from pIM130 obtained in Example 2 were analysed phenotypically by plating on MM containing 100 mM D-glucose. 100 mM D-glucose/1% Oat spelt xylan (Sigma #X0627) and 1% Oat spelt xylan. A selection of the transformants were replica plated to these media and incubated at 30° C. About 75% of the transformants were growing on xylan containing medium, while no growth was found on media containing D-glucose. The remaining 25% of the colonies grew on all three media tested.

A selection of five transformants having the expected phenotype (growth on xylan containing medium, non-growth on D-glucose containing media) was analysed by Southern analysis. Fungal DNA was isolated by a modified procedure used to isolate plant RNA essentially as described by de Graaff et al., 1988). Mycelium, which was grown overnight in culture medium, was harvested, washed with cold saline, frozen in liquid nitrogen and stored at −80° C. Nucleic acids were isolated by disrupting 0.5 g frozen mycelium using a microdismembrator (Braun). The mycelial powder obtained was extracted with freshly prepared extraction buffer. The extraction buffer was prepared as follows: 1 ml tri-isopropylnaphtalene sulfonic acid (TNS) (20 mg/ml) was thoroughly mixed with 1 ml p-aminosalicylic acid (PAS) (120 mg/ml) and 0.5 ml 5×RNB buffer was added (5×RNB contains 121.10 g Tris, 73.04 g NaCl and 95.10 g EGTA in 1 l, pH 8.5). After the addition of 1.5 ml phenol, the extraction buffer was equilibrated for 10 min. at 55° C. The warm buffer was then added to the mycelial powder, and the suspension was thoroughly mixed for 1 min. using a vortex mixer. After addition of 1 ml chloroform the suspension was remixed for 1 min. After centrifugation at 10⁴×g for 10 min., using a Sorvall high speed centrifuge, the aqueous phase was extracted once more with an equal volume of phenol/chloroform (1:1) and was then extracted twice with chloroform. DNA was isolated from the aqueous phase using the following procedure; the DNA was immediately precipitated from the aqueous phase with 2 vol. ethanol at room temperature and subsequently collected by centrifugation using a Sorvall high speed centrifuge at 10⁴×g for 10 min. and washed twice by redissolving the DNA in distilled, sterile water and precipitating it again with ethanol. RNA was removed by adding RNase A (20 g μg/ml) to the final solution.

High molecular weight DNA (1-2 μg) isolated from A. niger N402 (cspA1) as a wild-type and five pIM130 transformants as described was digested with HpaI (Life Technologies) according to the manufactors instructions. The resulting fragments were separated by agarose gel electrophoresis, and transferred to High-bond N membrane as described by Maniatis et al. (1982). Hybridisation using a ³²P-labelled 3.8 kb XbaI fragment, prepared as described by Sambrook et al., 1989, containing the A. niger pyrA gene as a probe was done according to the following procedure (Sambrook et al., prehybridization in 6×SSC (20×SSC per 1000 ml: 175.3 g NaCl, 107.1 g sodiumcitrate.5.5 H₂O. pH 7.0), 0.1% SDS, 0.05% sodium pyrophosphate, 5*Denhardt's solution (100×Denhardts solution per 500 ml: 10 g Ficoll-400, 10 g polyvinylpyrrolidone, 10 g Bovine Serum Albumin (Pentax Fraction V) and 20 μg/ml denatured herring sperm DNA at 68° C. for 3-5 hrs and hybridization in an identical buffer which contained the denatured radiolabelled probe at 68° C. for 15-18 hrs, followed by two washes in 3×SSC, 0.1% SDS at 68° C. and two washes in 0.2×SSC, 0.1% SDS at 68° C. The membrane was covered with Saran wrap and autoradiographed overnight at −70° C. using Konica X-ray films and Kodak X-Omatic cassettes with regular intensifying screens.

As a result a 10 kb hybridising band is found in the N402 lane, while this band is missing in the transformants NW205::130#1, NW205::130#2 and NW205::130#3. In the transformants NW205::130#1 and NW205::130#3 a 15 kb hybridising fragment is found, while in NW205::130#2 a 20 kb band is found. These results correspond respectively to a single and a double copy integration at the homologous pyrA locus. In the transformants NW205::130#4 and NW205::130#5 the plasmid was integrated at a non-homologous locus. Transformant NW205::130#2 was selected for mutagenesis.

The UAS fragment of pIM130 comprises the binding site required for the positive regulator to exhibit the stimulatory activity of the UAS. Thus inhibition of xlnR in the host cell comprising pIM130 will result in negative expression of the bidirectional marker present on pIM130. Expression of xlnR is induced by xylan or xylose. Thus the presence of such substrates should result in expression of the bidirectional marker of pIM130 if the host possesses xlnR.

The UAS fragment of pIM130 does not comprise the site required for inhibitory activity of creA that is present on the native UAS of the Aspergillus niger xlnA gene. Thus the presence of glucose which renders A. niger CRE A⁺ and subsequently inhibits the UAS of xlnA and the other xylanolytic enzyme encoding genes such as xlnD and axeA and also inhibits the xlnR gene encoding the activator of the UAS of the aforementioned xylanolytic enzyme encoding genes i.e. represses xylanolytic enzyme expression which results in negative expression of pIM130.

Example 4 Selection of Mutants Example 4.1 Selection of Derepressed Mutants

Spores of NW205::130#2 were harvested in 5 ml ST (ST: 0.8% NaCl, 0.05% Tween 20), shaken at high frequency and mycelial debris was removed by filtration over a sterile glasswool plug. The spores were collected by centrifugation for 10 minutes at 3000 rpm at room temperature in a bench centrifuge and were resuspended in 5 ml saline. This wash step was repeated twice and the spores were finally resuspended in saline at a density of 1*10⁷ per ml. 10 ml of the spore suspension was dispensed in a glass petridish and was irradiated using UV at a dosage of 18 erg/mm²/min for 2 min. After mutagenesis 10⁵ and 10⁶ spores were plated (10 plates each) on MM+10 mM L-arginine+10 μM nicotinamide containing 3% D-glucose and on plates containing 3% D-glucose/3% oat spelts xylan (Sigma #X0627).

After 4-7 days 5-10 mutant colonies per plate (10⁶ spores inoculated) were found which on basis of their morphology could be divided into three classes; large, well sporulating colonies, intermediate sized, well sporulating colonies and small poorly sporulating colonies. A random selection of 20 of these mutants was made and the selected mutants were tested on media containing different carbon sources or substrates. The mutant colonies were found to be able to grow on media containing D-glucose, D-glucose/xylan and xylan, while the parental strain NW205::130#2 only was able to grow on medium containing xylan as a carbon source. In addition these mutants were tested on different chromogenic substrates; 4-methylumbelliferyl-β-D-xyloside (β-xylosidases, endo-xylanases)(Sigma #M7008), 4-methylumbelliferyl acetate (acetyl-xylan esterases)(Sigma #M0883), 4-methylumbelliferyl-α-L-arabinofuranoside (arabinofuranosidases) (Sigma #M9519) and on Remazol Brilliant blue modified xylan (endo-xylanases)(Sigma #M5019). The methylumbelliferyl derivatives were added in a 1 mM final concentration to media containing D-glucose, D-glucose/xylan and xylan, while the RBB-xylan was added in a concentration of 1 mg/ml to media containing D-glucose/xylan and xylan. For all these substrates tested enzyme activity was found in the mutants after growth on D-glucose containing media, while no expression was found in the parental strain NW205::pIM130#2. On media containing xylan an increased expression of these enzymes was found in comparison to NW205::pIM130. Of the mutants tested mutant 5 B had the highest expression levels. In the instant case selection occurred on a substrate normally active as inhibitor of xylanolysis i.e. glucose. To be certain that expression could occur in the absence of repression an inducer of xylanolytic genes xylan was also included. Such a control test is preferably included in a method according to the invention. The mutant clearly exhibited derepression.

For the comparison of the activity levels produced, both A. niger N402 and mutant 5B were cultured on MM containing 1.5% crude Wheat arabino-xylan as a carbon source. Samples were taken at 24, 42, 72 and 96 hrs and the activities of α-L-arabinofuranosidase, endo-xylanase and β-xylosidase were measured. The results (FIGS. 2A,B,C) indicated an increase in activity for the mutant strain for all three enzymes. α-L-arabinofuranosidase and endo-xylanase activity was most strongly increased.

Example 4.2 Selection of Non-expressing Mutants

Spores of strain NW205::130#2 were harvested and mutated as described in Example 4.1 and subsequently plated on MM containing 100 mM D-xylose supplemented with 10 mM uridine, 10 mM L-arginin and 0.8 mg/ml 5-fluoroorotic acid (Sigma #F5013). These plates were incubated for 4-7 days at 30° C. 64 of the growing colonies, having a PYR⁻phenotype, were analysed for xylanase expression by plating on MM containing 1% xylan+10 mM uridine+10 mM L-arginin+10 μM nicotinamide. Of these 64 mutants tested 10 gave a reduced zone of clearing on these xylan containing plates and had potential reduced xylanase levels. The phenotype of these mutants was verified on D-glucose, D-glucose/xylan and xylan containing media in the presence and absence of uridine. All 10 mutants did not grow on media without uridine.

For further analysis these mutants were precultured 18 hrs at 30° C. on MM containing 50 mM fructose+10 mM uridine+10 mM L-arginin+10 μM nicotinamide after which the mycelium was harvested and 1 g wet mycelium was transferred to MM containing 1% xylan and to MM containing 10 mM D-xylose+10 mM uridine+10 mM L-arginine+10 μM nicotinamide. After 5.5 hrs incubation at 30° C. both the mycelium and the culture filtrate were harvested. The culture filtrate was dialysed against 1 mM Nap_(i) pH 5.6 after which the xylanase (Bailey et al. (1991)) was determined and β-xylosidase activities were determined (Table 1). Both the xylanase as well as the β-xylosidase expression levels were found to be strongly reduced in these selected mutants.

α-L-arabino- β-xylosidase furanosidase endo-xylanase xy- xy- xylan xylose xylan lose xylan lose Activity (nkat (nkat (nkat (nkat (nkat (nkat Strain ml⁻¹) ml⁻¹) ml⁻¹) ml⁻¹) ml⁻¹) ml⁻¹) NW205 5 * 10² 5 * 10¹ 0.35 0.40 0.33 0.37 NW205::130 5 * 10² 1 * 10² 0.36 0.51 0.40 0.29 NW205::130 2Ac2-15 5 * 10² 1 * 10² 0.26 0.30 0.30 0.23 NW205::130 Ac1-4 2 1 0.01 0.01 0.36 NW205::130 Ac4-4 2 0.3 0.01 0.01 0.24 NW205::130 Ac4-6 2 0.3 0.01 0.01 0.31 NW205::130 Ac3-14 1 0.4 0.01 0.01 0.29 NW205::130 Ac4-8 2 0.4 0.01 0.01 0.38 NW205::130 Ac2-10 1 0.1 0.01 0.01 0.19 NW205::130 Ac2-8 1 0.3 0.01 0.01 0.29 NW205::130 Ac2-5 1 0.2 0.01 0.01 0.28 NW205::130 Ac1-15 2 0.2 0.01 0.01 0.23 NW205::130 Ac4-14 2 0.2 0.01 0.01 0.28

Example 5 Complementation of Non-expressing Mutants 5.1 Construction of an A. niger Genomic Plasmid Library

For the construction of a plasmid library 10 μg of genomic DNA of A. niger NW128 (cspA1, nicA1, pyrA6, goxc17) isolated as described in Example 3, was partially digested for 30 min at 37° C. according to the manufactors instructions using 3.5 U Sau3A (Life-Technologies) in a final volume of 100 μl. After separation of the fragments by agarose electrophoresis, fragments ranging in size from 6.7 kb to 9.4 kb were cut from the low melting point agarose gel and were isolated as described in Sambrook et at., (1989). From totally 6 digestions 4 pg of fragments were isolated in a final concentration of 100 ng/μl. 600 ng of the resulting fragments were ligated in 100 ng BamHI digested pUC18 (Pharmacia #27526201) according to the manufacturers instructions. After ligation 4 μl of the resulting ligation mixture was used to transform 100 μl E. coli DH5α Max Efficiency competent cells (Life Technologies #18258-012) according to the manufactors instructions. Six subsequent transformation experiments resulted in about 5*10⁴ colonies. After resuspension of these colonies and growth for 3 hrs at 37° C. in TY medium (medium per 100 ml: 16 g Select Peptone 140 (Life Technologies), 10 g NaCl and 10 g Yeast extract) containing 100 μg/ml Ampicillin, plasmid DNA was isolated and purified by CsCl centrifugation.

5.2 Complementation of Non-expressing Mutants

For the complementation in non-expressing mutants a selection of three mutants, NW205::130 Ac1-4, NW205::130 Ac1-15 and NW205::130 Ac4-4, protoplasts were prepared of these strains and transformed as described in Example 2. In these transformation experiments 10⁸ protoplasts were used and combined with; 20 μg DNA of the A. niger plasmid library as described in Example 5.1, and with 10 μg DNA of the plasmid library combined with 10 pg DNA of the autonomously replicating plasmid pHELP1 (Gems and Clutterbuck, 1993) and with 20 μg DNA of the plasmid library combined with 10 μg DNA of the autonomously replicating plasmid pHELP1. As a positive control 2 μg pGW635 was used. After the transformation procedure the mixtures were plated on MM stabilised with 1.33 M Sorbitol containing 50 mM D-xylose as a carbon source supplemented with 10 μM nicotinamide and 10 mM L-arginin. After about 4 days colonies appeared on the positive control plates and were counted, while after 6 days colonies could be picked from the complementation plates.

The resulting transformant colonies were analysed by plating on medium containing 1% Oat spelt xylan, 1 mM 4-methylumbellyferyl-β-D-xyloside, 10 μM nicotinamide and 10 mM L-arginin. After 6-7 hrs incubation at 30° C. xx fluorescent colonies were detected. After 2-3 days a clearing of the xylan around these colonies appeared.

Example 6 Cloning of the A. niger xlnR Gene Example 6.1 Isolation of the A. niger xlnR Gene

The A. niger xlnR gene was isolated from transformants obtained and selected as described in Example 5.2. From 13 transformants obtained from NW205::130 Ac 1-4, NW205::130 Ac 1-15 and NW205::130 Ac 4-4 total DNA was isolated, as described by de Graaff et al., 1988. After mycelium was cultured under selective (i.e. inducing) conditions for pyrA and xylanolytic expression on 1.5% crude wheat arabino-xylan as C source from which free replicating plasmids were isolated using Nucleobond AX100 columns (Macherey & Nagel). 200 μg of total DNA dissolved in 400 μl of sterile water was mixed with 2 ml of S1 buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 100 μg RNase A), 2 ml of S2 (200 mM NaOH, 1% SDS), followed by an incubation at room temperature for 5 minutes, and 2 ml of S3 (2.60 M KAc, pH 5.2), followed by an incubation on ice for 5 minutes. After clearing of the suspension at 15.000 g for 30 minutes adsorption, washing, elution and precipitation of the plasmids was done all according to the manufacturers' instructions for “working procedure for the purification of plasmids and cosmids” (5.3 modified alkaline/SDS lysis). 20 μl of the resulting plasmid DNA, dissolved in 150 μl sterile water, was used in E. coli DH5α transformation. (Sambrook et al., 1989). 12 E. coli colonies resulting from each of these plasmid preparations were grown for 9-12 hrs at 37° C. in 250 ml LB medium containing 50 μg/ml Ampicillin, after which a miniprep plasmid DNA isolation was performed on 1.5 ml of the culture as described for the boiling lysis protocol by Sambrook et al., 1989 and the cells were pelleted by centrifugation and stored at −20° C. Analysis of these DNA preparations, after HinDIII digestion, by agarose 2electrophoresis revealed three classes of plasmids; pHELP1 type plasmids, genomic library type plasmids and large complex type plasmids. From colonies containing the latter type of plasmids, a large scale plasmid isolation, using Nucleobond AX100 columns according to the manufacturers' instructions for the modified alkaline/SDS lysis (Macherey-Nagel) was performed on the frozen pellet of the 250 ml culture. This resulted in the isolation of two plasmid types, A and B, complementant A and B respectively. Both these plasmids were digested, using SalI, PstI, EcoRI, HinDIII, and after agarose electrophoresis, the fragments were analysed in triplicate by Southern analysis using denatured radiolabelled pHELP1, plasmid A and plasmid B. This showed that both plasmids A and B, besides the pHELP part, shared the same genomic region. Based upon the differences between the hybridisation signals found using the pHELP plasmid, showing the vector and AMA1 sequences, and the plasmid A and B signals, fragments hybridising with both plasmid A and B, but not with pHELP1, were identified and subcloned. A 4 kb EcoRI fragment and a 6.5 kb HinDIII fragment of plasmid B, and a 3 kb PstI fragment of plasmid A were found to hybridise with both plasmids A and B and were subcloned in pGEM7/EcoRI, pGEM7/HinDIII and pBluescript/PstI, resulting in plasmid pNP1, 2 and 3 respectively. After propagation and purification these plasmids were used in complementation experiments using the mutant NW205::130 Ac 4-4 as described in Example 5.2. In these experiments the mutant was directly transformed without using pHELP1. In these experiments the plasmid pNP2, containing the 6.5 kb HinDIII fragment gave rise to complementation of the mutation. Further subcloning and transformation of pNP2-derived plasmids revealed a 5 kb BamHI-XbaI fragment, subcloned in pBluescript and resulting in plasmid pNP8, giving rise to complementation of strain NW205::130 Ac 4-4.

Example 6.2 Subcloning of the A. niger xlnR Gene

For the subcloning of the 2xlnR gene, the A. niger genomic library, constructed as described by Harmsen et al., 1990, was screened for phages containing the xlnR region by using the 4 kb EcoRI fragment of pNP1 as probe. 3×10³ pfu per plate were plated in NZYCM top-agarose containing 0.7% agarose on five 85-mm-diameter NZYCM (1.5% agar) plates as described (Maniatis et al., 1982) using E. coli LE392 as plating bacteria. After overnight incubation of the plates at 37° C. two replicas of each plate were made on HybondN⁺ filters (Amersham) as described in Maniatis et al. (1982). After wetting the filters in 3×SSC the filters were washed for 60 min. at room temperature in 3×SSC. Hybridisation using the ³²P-labelled 4 kb EcoRI fragment, prepared as described by Sambrook et al., 1989, was done according the following procedure (Sambrook et al., 1989); prehybridisation in 6×SSC (20×SSC per 1000 ml: 175.3 g NaCl, 107.1 g sodium citrate.5.5 H₂O. pH 7.0), 0.1% SDS, 0.05% sodium pyrophosphate, 5*Denhardt's solution (100×Denhardts solution per 500 ml: 10 g Ficoll-400, 10 g polyvinylpyrrolidone, 10 g Bovine Serum Albumin (Pentax Fraction V) and 20 μg/ml denatured herring sperm DNA at 6° C. for 3-5 hrs and hybridisation in an identical buffer which contained the denatured radiolabelled probe at 68° C. for 15-18 hrs, followed by two washes in 2×SSC, 0.1% SDS at 68° C. and two washes in 0.2×SSC, 0.1% SDS at 68° C. The membrane was covered with Saran wrap and autoradiographed overnight at −70° C. using Konica X-ray films and Kodak X-Omatic cassettes with regular intensifying screens.

This screening resulted in about 12 positive phages, of which eight were purified. Each positive plaque was picked from the plate using a Pasteur pipette and the phages were eluted from the agar plug in 1 ml of SM buffer containing 20 μl chloroform, as described in Maniatis et al. (1982). The phages obtained were purified by repeating the procedure described above using filter replicas from plates containing 50-100 plaques of the isolated phages.

After purification the phages were propagated by plating 5×10³ phages on NZYCM medium. After overnight incubation at 37° C. confluent plates were obtained, from which the phages were eluted by adding 5 ml SM buffer and storing the plate for 2 h. at 4° C. with intermittent shaking. After collection of the supernatant using a pipette, the bacteria were removed from the solution by centrifugation at 4,000×g for 10 min. at 4° C. To the supernatant 0.3% chloroform was added and the number of pfu is determined. These phage stocks (A-R/H-R) contain approximately 10⁹ pfu/ml.

DNA of five selected phages, A-R,B-R,C-R,E-R,F-R, isolated as described in Sambrook et al. (1989), was analysed by Southern analysis. The DNA was digested for 5 h. at 37° C. in a reaction mixture composed of the following solutions; 5 μl (=1 μg) DNA solution; 2 μl of the appropriate 10×React buffer (Life Technologies); 10 U Restriction enzyme (Life Technologies) and sterile distilled water to give a final volume of 20 μl. The samples were incubated for 10 min. at 65° C. and rapidly cooled on ice, before loading on a 0.6% agarose gel in 1*TAE buffer. The DNA fragments were separated by electrophoresis at 25 V for 15-18 h.

After electrophoresis the DNA was transferred and denatured by alkaline vacuum blotting (VacuGene XL, Pharmacia LKB) to nylon membrane (Hybond N, Amersham) as described in the VacuGene XL instruction manual (pp. 25-26) and subsequently prehybridised and hybridised using the denatured radiolabelled 5 kb BamHI-XbaI fragment of plasmid pNP8 with hybridisation conditions as described. The hybridisation pattern was obtained by exposure of Kodak XAR-5 X-ray film for 18 h. at −70° C. using a regular intensifying screen. In all 5 clones, fragments originating from the same genomic region were found, for which a restriction pattern was constructed.

Based on the restriction map a 5 kb BamHI-XbaI fragment was selected for subcloning. 100 ng pBluescript BamHI-XbaI digested vector was mixed with 250 ng 5 kb BamHI-XbaI DNA of phage B-R and 4 μl 5*ligation buffer (composition; 500 mM Tris-HCl, pH 7.6; 100 mM MgCl_(2; 10) mM ATP; 10 mM dithiotreitol; 25% PEG-6000), and 1 μl (1.2 U/μl) T₄ DNA ligase (Life Technologies) was added to this mixture in a final volume of 20 μl. After incubation for 16 h at 14° C. the mixture was diluted to 100 μl with sterile water. 10 μl of the diluted mixture was used to transform E. coli DH5α competent cells, prepared as described by Sambrook et al. (1989). Six of the resulting colonies were grown overnight in LB medium (LB medium per 1000 ml: 10 g trypticase peptone (BBL), 5 g yeast extract (BBL), 10 g NaCl, 0.5 mM Tris-HCl pH 7.5) containing 100 μg/ml ampicillin. From the cultures plasmid DNA was isolated by the boiling lysis method as described by Maniatis et al. (1982), which was used in restriction analysis to select a clone harbouring the desired plasmid pIM230. Plasmid DNA was isolated on a large scale from 500 ml cultures E. coli DH5α containing pIM230 grown in LB medium containing 100 μg/ml ampicillin (Maniatis et al., 1982) The plasmid was purified by CsCl centrifugation, ethanol precipitated and dissolved in 400 μl TE. The yield was approximately 500 μg. E. coli containing pIM230 was deposited at the CBS under the conditions of the Treaty of Budapest on June 1996 under the accession number CBS 678.96.

Example 6.3 Subcloning of the A. niger xlnR cDNA

To obtain a cDNA clone of part of the zinc finger regio of the xlnR gene, a reverse transcriptase and second strand synthesis reaction were carried out on 1 μg of polyA⁺ RNA from an A. niger N402 wild-type strain grown on xylan for 30 hrs with an oligonucleotide starting at position 1476-1496 (Seq id no 9), in analogy to the method as described in the ZAP™-cDNA synthesis kit (Stratagene). An aliquot (1/50) of the second strand reaction was used as template in PCR with primer R026 and R025 (derived from positions 946-970 of Seq id no 9) in 35 cycles of 60 seconds of subsequent 95° C. 58° C. and 72° C., followed by an incubation of 5 minutes at 72° C. The resulting fragment of 500 bp was subcloned in the pGEM-T vector (Promega) and sequenced.

Example 7 The Primary Structure of the xlnR Gene Example 7.1 Sequence Analysis of the xlnR Gene

The sequence of the A. niger xlnR gene, its promoter/regulation region, the structural part of the gene and the termination region. was determined by subcloning fragments from both pNP8 as pIM230, in combination with the use of specific oligonucleotides as primers in the sequencing reactions.

For nucleotide sequence analysis restriction fragments were isolated and were then cloned in pEMBL, pUC, pBluescript, pGEM DNA vectors, digested with the appropriate restriction enzymes. The nucleotide sequences were determined by the dideoxynucleotide chain-termination procedure (Sanger et al., 1977) using the Pharmacia ALF express automated sequencer and the Thermosequenase sequencing kit (Amersham). In the case of gene specific oligonucleotides the Pharmacia Cy5 internal labelling kit was used in combination with the T7 DNA polymerase sequencing kit (Pharmacia). The reactions and the electrophoresis was performed according to the manufacturers' instructions. Computer analysis was done using the PC/GENE programme (Intelligenetics). The sequence determined is given in SEQ ID NO:9.

Example 7.2 Description of the xlnR Gene

The sequence as given in SEQ ID NO:9, comprising the xlnR structural gene, is preceded by a 947 nucleotide long upstream region. In the upstream non-coding region CT-enriched sequences are found but no TATAA box. The structural part of the xlnR gene ranges from position 948 till position 3690. interrupted by two introns. The intron at position 1174 till 1237 was certified by sequencing the genomic fragment in pIM230, described in example 6.2 and part of the cDNA, as described in example 6.3. A second intron is indicated from position 3496 till position 3549. The second intron sequences follow the conserved intron sequences, normally found in fungi, for splice junctions and lariat sequence.

The xlnR gene encodes a protein of 875 amino acids in length. The derived polypeptide contains a typical N-terminal zinc binuclear cluster domain encoded by nucleotides from position 1110 till position 1260, with typical six cysteines coordinating the zinc. In this region futhermore a number of similarities with other fungal regulatory proteins are shown as listed in e.g. FIG. 1 of Kraulis et al. (1992) which is herein incorporated by reference.

A typical RRRLWW motif is found from position 2623 till position 2649, this motif is found. with slight variations, in a number of binuclear zinc cluster regulatory proteins as noted by Suárez et al. (1995).

Example 7.3 Sequence Analysis of xlnR in A. niger Mutants

To determine whether the mutation, in the case of the A. niger mutants which do not express the xylanolytic system, as described in example 4.2, is located in xlnR, the sequence of the xlnR gene of these mutants was determined. For this a library enriched for 5.5 kb BamHI xlnR containing fragments was made for each of the NW205::130 Ac mutants. For the construction of this xlnR enriched library. 5.5 kb fragments of BamHI, HinDIII, XhoI, SstI and KpnI digested genomic DNAs were isolated for each strain. These fragments were mixed with BamHI digested, dephosphorylated pUC18 vector (Ready-To-Go™ pUC18 BamHI/BAP+Ligase, Pharmacia) and ligated. The ligation mixture was used to transform E. coli DH5α (MAX Efficiency DH5α™ Competent Cells, Gibco-BRL) for Amp resistance according to the manufacturers' protocol, which resulted in a primary library of 5*10²-10³ colonies. These A. niger xlnR enriched libraries, after replating the primary library on master plates, were screened by colony filter hybridisation according to standard protocol (Sambrook et al., 1989), with the use of the denatured radiolabelled BamHI-XbaI insert of pIM230 as a probe.

For each mutant strain, positive colonies were picked from the master plate with a toothpick and were grown for 15-18 hrs at 37° C. in 5 ml LB medium containing 100 μg/ml Ampicillin, after which a miniprep plasmid DNA isolation was performed as described for boiling lysis by Sambrook et al. (1989). Analysis of these DNA preparations by agarose electrophoresis and comparing digestion patterns with zlnR specific patterns revealed colonies containing the correct 5.5 kb BamHI xlnR fragment. The sequence of the A. niger mutants was determined with the use of specific zlnR oligonucleotides as primers in the sequencing reactions as described in example 7.2. For mutant NW205::130 Ac 1-15 a single basepair substitution was determined at position 3479, resulting in the change of the Leucine at position 823 of SEQ ID NO:9 into a Serine. For mutant NW205::130 Ac 2-5 a single basepair substitution was determined at position 3655, resulting in the change of the Tyrosine at position 864 of SEQ ID NO:9 into an Aspartic acid. These mutations identify both mutants as xlnR mutants.

Example 8 Expression of xlnR in A. niger Example 8.1 Complementation of A. niger Mutants Non-expressing the Xylanolytic System

For the complementation in all non-expressing mutants all ten NW205::130 Ac mutants, as described in Example 4, were transformed as described in example 2 of this document by combining protoplasts and pGW635 as a control for transformation frequency and pIM230 DNA for testing the complementation ability of pIM230.

The resulting transformant colonies were analysed for xylanolytic activity and compared with their parental mutant strain, by plating them on appropriate medium containing 1% oat spelts xylan as C source, and after 2-3 days a clearing of the xylan around the transformant colonies, but not the parental mutant strain, appeared for all ten, thereby showing the restoration of xylanolytic activity.

Example 9 Effect of xlnR Gene Dosage on the Expression of the A. niger Xylanolytic System

To study the potential use of the xlnR gene for strain improvement for an increased xylanolytic expression, the strain N902::200-18, harbouring multiple copies (about 6) of the A. niger xlnD gene encoding β-xylosidase, was transformed to arginine prototrophy in a co-transformation experiment, as described in Example 2 of this document using 19 μg of the xlnR harbouring plasmid pIM230 and 2 μg of the plasmid pIM650 harbouring the A. nidulans argB gene (Johnstone et al., 1985). The transformants obtained were screened for increased endo-xylanase expression, on MM plates containing 1% Oat spelts xylan. Four colonies, having the fastest and largest halo formation, were selected to determine xlnR copy numbers. For this DNA of these transformants and the recipient strain, was isolated and serial dilutions were spotted onto Hybond N membrane. The copy number was estimated from the signals found after hybridisation, using a radiolabelled 4.5 kb SmaI/XbaI fragment spanning the coding sequence of the xlnR gene. Based on comparison to the recipient strain the xlnR copy number was determined to be 8 in N902::200-18-R14 and 32 in N902::200-18-R16. For both these transformants the effect of the increased gene dosage of xlnR was analysed by Northern analysis after strains were grown in liquid culture. This was done in a transfer experiment into 2% oat spelts xylan as a carbon source, after a preculture in 1% fructose for 18 h. Mycelial samples were taken 8 and 24 hrs after transfer, from which total RNA was isolated using TriZol (Life technologies) according to the manufacturers instructions and analysed by Northern blot analysis (Sambrook et al., 1989). Xylanase B expression levels were strongly increased in these transformants in comparison to the recipient strain, as detected after hybridisation using the radiolabelled 1 kb EcoRI/XhoI fragment of A. niger xlnB (Kinoshita et al., 1995).

To further study the potential use of the xlnR gene for strain improvement for an increased endo-xylanase expression. A. niger was transformed, as described in Example 2 of this document according to the following scheme; 1. pGW635 (pyrA) (positive control), 2. pDB-K(XA), 3 pDB-K(XA)+pIM230) and 4 pGW635+pIM230. The plasmid pDB-K(XA) contains both the A. niger pyrA gene and the A. niger xylanase A gene from A. tubigensis in the vector pEMBL18. Transformants were obtained for all conditions used strains overexpressing endo-xylanases were selected by halo size in a plate screening on Oat spelts xylan (20 transformants from each group were tested).

From each group one transformant was selected and grown for activity assays. The strains were pregrown for 18 hrs on medium containing fructose, after which the mycelium (2.5 g wet weight in 50 ml) was transferred to medium containing 1.4% crude arabino xylan. All cultures were performed in shake flasks. Incubations were done for 40 hrs at 30° C. and the xylanase A levels were determined by HPLC analysis, while β-xylosidase and endo-xylanase activities were determined for both. Chromatography was carried out on standard Pharmacia-LKB HPLC equipment (Uppsala, Sweden) running a SOURCE 15 Q, HR 5/5-column at 1.5 ml/min. Buffer A=20 mM TRIS-buffer, pH 7.5 and buffer B=20 mM TRIS-buffer, pH 7.5 with 1M NaCl. Gradient from 0-50% buffer B over 30 min. Detection at 280 nm, Pharmacia-LKB UV-MII, absorbance range at 0.1-0.2, see FIG. 3. 100 μl culture media was diluted with 1000 μl 20 mM TRIS-buffer, pH 7.5 and 1000 μl diluted sample was applied to the column. The xylanase A activity is then seen as a peak eluting at approx. 30% B-buffer. From each group of transformants the one showing the highest xylanase A activity/peak in the HPLC analysis is shown in FIG. 3. The endo-xylanase activity was determined by measuring the release of dyed fragments from azurine-dyed cross-linked wheat arabinoxylan (Xylazyme tablets) from Megazyme, Warriewood, Australia. The xylanase activity was calculated by comparing with an internal standard enzyme of 100 XU/gram (Xylanase-Unit) at 40° C. in 0.1 M acetate buffer. pH 3.4. The same four transformants were assayed on water insoluble arabinoxylan at a pH were only xylanase A contributes to the endoxylanase activity, the results of this analysis is given in table 2.

TABLE 2 Transformant XU/gram pyr + (control) 4 DB-K(XA)-15 52 DB-K(XA)/pIM230-21 111 pIM230-26 24

From the results shown in FIG. 3 and table 2 it is clear that transformation with the xylanase A encoding gene as expected gives a large increase in the xylanase A enzyme activity. More surprisingly, also after transformation using the activator gene xlnR, also a large increase in the level of xylanase A is found. This indicates a limitation in the level of activator XYL R (=xlnR gene product) in the untransformed parent. Therefore, it is expected that in a pDB-K(XA) multicopy transformant the amount of transacting regulatory factor will be even more limiting. This is confirmed by the result for the pDB-K(XA)/pIM230 transformant, which has a xylanase A level twice as high as the pDB-K(XA) multicopy transformant.

Example 10 Screening Filamentous Fungi for the xlnR Gene

To analyse whether it is possible to isolate the xlnR counterpart from other fungi by heterologous hybridisation, using the 4.5 kb SmaI/XbaI fragment of the xlnR gene as a probe. DNA was isolated from the following strains; A. niger N902 (argB15, cspA1, fwnA1, metB10, pyrA5), A. tubingensis NW184 (cspA1, fwnA1, pyrA22), A. nidulans WG096 (pabaA1, yA2) of FGSC 187, A. aculeatus NW240 (pyrA3) of CBS 101.43, A. aculeatus NW217 (fwnA1, cspA1, pyrA4, lysA1) of CBS 115.80, A. foetidus (awamori) NW183 (cspA1, fwnA1, pyrA13, lysA1) of CBS 115.52, A. japonicus CBS 114.51 and Trichoderma reesei QM9414. 1-2 μg DNA was digested with BamHI or with XhoI and subsequently analysed by Southern analysis as described in Example 3. The hybridisation conditions used were: hybridisation in 6×SSC (20×SSC per 1000 ml: 175.3 g NaCl, 107. 1 g sodium citrate. 5.5H₂O, pH 7.0), 0.1% SDS, 0.05% sodium pyrophosphate, 5*Denhardt's solution (100×Denhardt's solution per 500 ml: 10 g Ficoll-400, 10 g polyvinylpyrrolidone, 10 g Bovine Serum Albumin (Pentax Fraction V) and 20 μg/ml denatured herring sperm DNA at 56° C. for 18-24 hrs followed by two 30 min. washes in 5×SSC, 0.1% SDS at 68° C. and two 30 min. washes in 2×SSC, 0.1% SDS at 56° C. After hybridisation the membrane was covered with Saran wrap and autoradiographed overnight at −70° C. using Konica X-ray films and Kodak X-Omatic cassettes with regular intensifying screens.

As a result hybridising fragments were found for all fungi analysed, very strong hybridisation signals were found in A. niger, A, tubigensis, A. foetidus, while in the other strains investigated clear hybridisation signals were found.

Example 11 Application of the Selection System Using Other Promoter Fragments

Plasmids were constructed containing promoter fragments from the A. niger abfA gene (Flipphi et al., 1994) and the A. niger abfB gene (Flipphi et al., 1993). For the construction containing the abfA promoter fragment, a 1.4 kb XhoI/PstI fragment from pIM900 (Flipphi et al., 1994) was ligated in SalI/PstI digested pAlter (Promega), as described in Example 1. Using the Altered Sites II in vitro mutagenesis system (Promega) a XhoI restriction site was created at positions −83 till −88 relative to the translation initiation site (Flipphi et al., 1994). From the resulting plasmid a 953 bp SstI/XhoI fragment was isolated. This fragment and a 1.5 kb XhoI fragment from pIM130 were ligated into pBluescript (Stratagene) digested with SstI/XhoI. Plasmids containing the correct orientation of the 1.5 XhoI fragment were identified by a digestion using BglII. The resulting plasmid is pAP8.

Analogously a 910 bp PstI fragment from the abfB promoter was isolated from pIM991 (Flipphi et al., 1993) and ligated in PstI digested pEMBL19. The resulting plasmid was digested using SalI and was ligated with the 1.5 kb XhoI fragment from plasmid pIM130. Plasmids containing both fragments in the correct orientation were identified by a digestion using BamHI. The resulting plasmid is pIM132.

A third plasmid containing a fragment from the A. niger pgaII was constructed by cloning a 1450 bp XbaI/XhoI fragment into the vector pAlter. Using the Altered Sites II in vitro mutagenesis system (Promega) a XhoI restriction site was created at positions −107 till −112 relative to the translation initiation site (Bussink et al., 1991). From the resulting plasmid a 1.2 kb XbaI/XhoI fragment was isolated. This fragment and a 1.5 kb XhoI fragment from pIM130 were ligated into pBluescript (Stratagene) digested with XbaI/XhoI. Plasmids containing the correct orientation of the 1.5 XhoI fragment were identified by a digestion using HinDIII. The resulting plasmid is pIIP7. From the same pgaII gene a 223 bp HinDIII/PstI fragment (Bussink et al., 1992) was isolated and ligated in HinDIII/PstI digested pEMBL19. The resulting plasmid was digested using SalI and was ligated with the 1.5 kb XhoI fragment from plasmid pIM130. Plasmids containing both fragments in the correct orientation were identified by a digestion using HinDIII. The resulting plasmid is pHPII.

All four plasmids were introduced in A. niger NW219 by transformation as described in Example 2, using 10 mM L-arabitol as an inducer in transformation experiments using the constructs having the abf promoter fragments (plasmids AP8 and pIM132) and 1% polygalacturonic acid (USB chemicals) in the case of the plasmids harbouring the pgaII fragments. While for the plasmids AP8 and pIM132 transformants were found at high frequency, for the transformation experiment using the pgaII promoter fragment containing plasmids pIIP7 and pHPII only 5 and 7 transformants were found respectively.

The transformants resulting from the transformation experiment using the plasmids pAP8 and pIM132 (abf promoter fragments were analysed phenotypically as described in Example 3 using MM containing 10 mM L-arabitol/50 mM sorbitol, 10 mM L-arabitol/50 mM D-glucose and 50 mm D-glucose. The expected phenotype; growth on 10 mM L-arabitol/50 mM sorbitol, non-growth on 10 mM L-arabitol/ 50 mM D-glucose and 50 mM D-glucose, was found for 10 out of 29 transformants resulting from plasmid pAP8 and 13 out of 30 transformants resulting from plasmid pIM132. The transformants resulting the plasmids pIIP7 and pHPII were tested on MM containing 1% polygalacturonic acid, 1% polygalacturonic acid/50 mM D-glucose and 50 mM D-glucose. Both classes of transformants however, did not show the expected phenotype, all transformants were able to grow on all three media. This suggests that these transformants result from a double cross-over at the pyrA locus.

Based on the results for the pgaII promoter fragment containing plasmids, we have tested whether we could improve transformation frequency by improving induction. We assumed that transformation more or less failed due to lack of inducer, since no monomeric inducer for polygalacturonases was available and thus the polymer needs to be degraded to release inducer to give expression. We tested whether supplementation of the medium using a small amount of uridin could overcome this problem. For this the NW219 and a transformant NW219::pIM132#30 were tested on media containing 1% Oat spelts xylan, giving induction of abfB, in combination with an increasing amount of uridin; respectively 0.0.001, 0.005, 0.01, 0.1, 1, 5 and 10 mM. In this experiment the recipient strain NW219 did not grow on media containing less then 0.01 mM uridin, while the NW219::pIM132#30 transformant strain grew under all conditions used. However, the degree of sporulation and colony morphology varied, the lowest uridin concentration giving wild-type-like sporulation being around 0.01 mM uridin. Based on these results A. niger NW219 transformation using the plasmids pIIP7 and pHPII was repeated using MMS as described in Example 2 containing 1% lemon pectin (degree of esterification 45%) (Copenhagen Pectin factory) and two conditions for uridin supplementation 0.01 mM and 0.005 mM respectively. This resulted in an increased number of transformants found. These transformants were tested on media containing 1% lemon pectin as described above, 1% lemon pectin/50 mM D-glucose and 50 mM D-glucose, for which the expected phenotype is respectively growth, non-growth and non-growth. For the pIIP7 resulting transformants 10 out of 30 transformants and for the pHPII 9 out 30 transformants the expected phenotype was found.

A selection of the transformants showing the expected phenotype were analysed by Southern analysis. DNA was isolated and analysed as described in Example 3. For the transformants resulting from the abfA promoter fragment containing plasmid pAP8 the DNA was digested using ClaI, for pIM132 (abfB) resulting transformants using ClaI and for the transformants resulting from pgaII plasmids pIIP7 and pHPII using ClaI. Based on the autoradiograph obtained after hybridisation using the following radiolabelled fragments; the 3.8 kb XbaI and the 1.2 kb ClaI fragment of the pyrA gene, transformants were selected based on estimated copy number. The following transformants were selected; AP8/16 (abfA), NW219::132#8 (2 copies) and NW219::132#30 (3-4 copies) (abfB), NW219::pIIP7#3 (2 copies) and NW219::pHPIIP#9 (2 copies) (pgaII)

The selected transformants were subjected to mutagenesis as described in Example 4. Arabinofuranosidase derepressed mutants were selected on MM+50 mM D-glucose and on MM+10 mM L-arabitol/50 mM D-glucose, while polygalacturonase derepressed mutants were selected on MM+50 mM D-glucose and on MM+1% lemon pectin/50 mM D-glucose. After 4-7 days 5-10 mutant colonies per plate were found, which on basis of their morphology could be divided into three classes; large, well sporulating colonies, intermediate sized, well sporulating colonies and small poorly sporulating colonies. A random selection of 20 of these mutants was made and the selected mutants were tested on media containing different carbon sources or substrates. The arabinofuranosidase mutant colonies were found to be able to grow on media containing D-glucose. D-glucose/L-arabitol and L-arabitol, while the parental strains only were able to grow on medium containing L-arabitol as a carbon source. Analogously the polygalacturonase mutants also were able to grow on MM+50 mM D-glucose and on MM+1% lemon pectin/50 mM D-glucose and MM+1% lemon pectin. The parental strains could only grow on MM+1% lemon pectin. In addition the arabinofuranosidase mutants (20 of each) were tested on the chromogenic substrate methylumbelliferyl-α-L-arabinofuranoside as described in Example 4. While the parental strains did not show any arabinofuranosidase expression of D-glucose/L-arabitol containing media, as detected by fluorescence of the substrate, the mutants showed variable levels of expression, the highest levels were found in mutants selected on the D-glucose medium.

The polygalacturonase mutants were tested on MM+1% lemon pectin/50 mM glucose, two and three days after inoculation of the plates polygalacturonase activity was visualized by staining as described by Ried and Collmer (1985). In this case for the parental strain a small halo was found, while in the mutants various degrees on increased halo formation was detected.

According to Example 4 also non-expressing mutants were selected on media containing FOA. For this strains NW219::132#30(abfB) were mutated and plated on MM+10 mM L-arabitol+1 mg/ml FOA+10 mM uridin. After 7-10 days mutants were selected and plated to MM containing 10 mM L-arabitol/50 mM sorbitol, 10 mM uridin and having a top agar containing 0.5% AZCL-arabinan (Megazyme, Sydney, Australia) for the detection of endo-arabinan expression. Two of the 30 transformants tested, 132/30 F12 and F26, were not able to release the dye from the substrate, an indication for the absence of endo-arabinan activity. Upon cultivation of these transformants in liquid MM containing 10 mM L-arabitol and 10 mM uridin and subsequent measurement of arabinofuranosidase activity in the culture filtrates, an at least 4-fold decrease in activity was found.

The strain NW219::pIIP7#3 was mutated and plated on MM containing 1% lemon pectin/50 mM sorbitol, 10 mM uridin and 1 mg/ml FOA. After incubation of the plates for 6-10 days mutants were picked and screened for polygalacturonase activity as described above. Of 65 mutants selected three mutants were found to have a decreased haloformation after polygalacturonase activity staining. indicating a decrease in polygalacturonase expression.

Examples 7, 8 and 11 of EP 95201707. 7, which is a copending European patent application of which a copy has been included upon filing the subject document and which examples have also been copied into this document.

Example 7 of EP 95201707. 7 Transformation of A. niger Using the Plasmid pIM200

250 ml of culture medium, which consists of MM supplemented with 2% glucose, 0.5% Yeast Extract. 0.2% Casamino acids (Vitamin free). 2 mM leucine, 10 μM nicotinamide, 10 mM uridine, was inoculated with 1*10⁶ spores per ml of strain NW155 (cspA1, argB13, pyrA6, nicA1, LeuA1, prtF28) (derived from NW228. Van den Hombergh et al, 1995) and mycelium was grown for 16-18 hours at 30° C. and 250 rpm in a orbital New Brunswick shaker. The mycelium was harvested on Myracloth (nylon gauze) using a Buchner funnel and mild suction and was washed several times with SP6 (SP6: 0.8% NaCl, 10 mM Na-phosphate buffer pH 6.0). 150 mg Novozyme 234 was dissolved in 20 ml SMC (SMC: 1.33 M sorbitol, 50 mM CaCl₂, −20 mM MES buffer, pH 5.8) to which 1 g (wet weight) mycelium was added and which was carefully resuspended. This suspension was incubated gently shaking for 1-2 hours at 30° C., every 30 minutes the mycelium was carefully resuspended and a sample was taken to monitor protoplast formation using a haemocytometer to count the protoplasts. When sufficient protoplasts were present (more then 1*10⁸) these were carefully resuspended and the mycelial debris was removed by filtration over a sterile glasswool plug. The protoplasts were collected by 10 minutes centrifugation at 3000 rpm and 4° C. in a bench centrifuge, the supernatant was removed and the pellet was carefully resuspended in 5 ml STC (STC: 1.33 M Sorbitol, 50 mm CaCl₂, 10 mM Tris/HCl, pH 7.5). This wash step was repeated twice and the protoplasts were finally resuspended in STC at a density of 1*10⁸ per ml.

The transformation was performed by adding 20 μg of pIM200 DNA and 5 μg pGW635, containing the A. niger pyrA gene (dissolved in a 10-20 μl TE), to 200 μl of protoplast suspension together with 50 μl of PEG buffer (PEG Buffer: 25% PEG-6000, 50 mM CaCl₂, 10 mM Tris/HCl pH 7.2), mixed gently by pipetting up and down a few times, and incubated at room temperature for 20 minutes. After this period 2 ml PEG buffer was added, the solution was mixed gently and incubated at room temperature for another 5 minutes and subsequently 4 ml of STC was added and mixed gently on a vortex mixer. One ml portions of this suspension were then added to 4 ml of 0.95 M sucrose osmotically stabilised top agar and poured on osmotically stabilised plates. As a control A. niger was also transformed using pGW635.

Example 8 of EP 95201707. 7 Analysis of Transformants

The transformants from pIM200 obtained in Example 7 were analysed phenotypically by plating on MM containing 1% Oat spelt xylan and 1 mM 4-methylumbelliferyl-D-β-xyloside. Of the 26 transformants tested, five had an increased fluorescence. These transformants, together with a PYR⁺ transformant as a reference, were grown on MM containing 1% Oat spelt xylan for 20, 27 and 42 hrs, after which the β-xylosidase activity towards PNP-X was measured. The results are summarised in Table C.

An increased level of β-xylosidase activity was found in all five transformants selected, the highest level being more then 30 times the wild-type activity. These results were confirmed by Western blot analysis, using the anti β-xylosidase antibody. prepared as described in Example 3 of the EP 95201707. 7, and the Bio-Rad Immun-blot GAR-AP assay kit following the suppliers instructions.

TABLE C β-xylosidase activities in A. niger transformants activity (mU/ml culture filtrate) after: 20 hr 27 hr 42 hr pGW 635 15  16 17 XlsA1 82  86 51 XlsA4 90 112 78 XlsA8 211  239 384  XlsA9 63 110 74 XlsA12 96 295 527 

Example 11 of EP 95201707. 7: Disruption of the A. niger xlnD gene Example 11.1 Construction of the Disruption Plasmids pIM203 and pIM204

The gene disruption plasmids pIM203 and pIM204 were constructed by generating an internal fragment of the xlnD gene by PCR. The fragment was generated using the oligonucleotides derived from the xlnD sequence (SEQ ID NO: 8). Xylos001 was derived from positions 1157 till 1176 and xylos004. was derived from positions 3147 till 3164. The fragment was generated by PCR containing 10 μl 10*reaction buffer (100 mM Tris-HCl, pH 8.3, 500 mm KCl, 15 MM MgCl₂, 0.01% gelatine), 16 μl 1.25 mM of each of the four deoxynucleotide triphosphates. 1 ng of the plasmid pIM200 DNA and 1 μg of each of the oligonucleotides in a final volume of 100 μl. This reaction mixture was mixed and 1 μl TAQ polymerase (5 U/μl) (Life Technologies) was added. The DNA was denatured by incubation for 3 min at 92° C. followed by 25 cycli of 1 min 92° C., 1.5 min 52° C. and 1.5 min 72° C. After these 25 cycli the mixture was incubated for 5 min at 72° C. Analysis of the reaction products by agarose electrophoresis revealed a fragment of about 2000 bp, which corresponds to the size expected, based on the sequence of the gene. The resulting fragment was subcloned in the vector pGEM-T (Promega) resulting in the plasmid pIM202. Plasmid pIM203 was constructed by ligation of a Smal/Pstl fragment of pILJ16 (Johnstone et al., 1985), containing the A. nidulans arg B gene (Upshall et al., 1986), in the EcoRV/Pstl digested pIM202 vector. Plasmid pIM204 was constructed by ligation of the Nsfl/Xbal fragment of pIM130 (this document, EP 95202346. 3), containing the pyrA gene under the control of the UAS of the xlnA promoter of A. tubigensis, in the Spel/Nsil digested pIM202 vector.

Example 11.2 Disruption of the xlnD Gene in A. niger

The plasmids containing the xlnD internal fragment as well as the argB gene (pIM203) or the pyrA gene (plM204), as described in Example 11.1 of the copending EP application, as a selection marker in transformation, were used to disrupt the A. niger xlnD gene. For this A. niger N902 (argB15, cspA1, fwnA1, metB10, pyrA5) was transformed, as described in Example 2 of this document, using the plasmids pIM203 and pIM204 selecting for arginine or uridine prototrophy respectively. The resulting transformants were screened for activity on methylumbelliferyl-β-D-xyloside on a 1% xylan plate as described in Example 8 of the copending EP application. For both groups of transformants twenty were screened. Of these transformants one of each group had a severe decreased level of MUX activity after 24 h of growth. Southern analysis of the selected transformants, as described in Example 3 of the copending application, demonstrated for the pIM203 transformant a multicopy integration at the homologous xlnD locus. In case of the pIM204 transformant a single homologous integration at the xlnD locus had occurred. Analysis for PNP-X activity. as described in Example 8 of the copending EP application, of these transformants revealed an at least 100-fold decrease in β-xylosidase activity.

Example 11.3 Effect of Overexpression and Inactivation of xlnD Gene on the Expression of Xylanolytic System of A. niger

To determine the effect of xlnD expression on the expression of the xylanolytic spectrum, A. niger N902. two xlnD multicopy-transformants in N902 and the xlnD gene disruption strains were grown in liquid culture. This was done in a transfer experiment into 2% oat spelts xylan or 3% D-xylose as a carbon source, after a preculture in 1% fructose for 18 h. Beta-xylosidase activity was determined as PNP-X activity in the culture filtrate. With both C sources a clear overexpression could be seen for the pIM200 transformants against an almost absence of PNP-X activity for both (pIM203 and pIM204) inactivation transformants. The xlnD gene disruption transformants showed an initial decreased level of endo-xylanase expression, which however increased in time finally after 16 hrs resulting in increased activity levels in comparison to the A. niger wild-type. Thus resulting in xylanase preparations free of β-xylosidase.

The culture filtrates were subsequently analysed by HPLC analysis. using a Dionex system and Pulsed Amperometric Detection. For this 1 ml of culture filtrate was boiled immediately after harvesting, to inactivate the xylanolytic enzymes, after which the sample was centrifuged for 10 min. (14,000 rpm at 4° C., Eppendorf centrifuge). The resulting supernatant was diluted 5-fold in bidest and 20 μl was analysed by HPLC using a Dionex CarboPac 100 column. The analysis indicated that, while in the wild-type and in the over-expression transformants only in the initial stage xylose oligomers could be detected in the culture filtrate, in the disruption mutant xylobiose and to a lesser extent xylotriose accumulated in the culture filtrate, thus resulting in a source for xylooligomers, in particular xylobiose and xylotriose.

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SEQUENCE LISTING (1) GENERAL INFORMATION: (iii) NUMBER OF SEQUENCES: 10 (2) INFORMATION FOR SEQ ID NO: 1: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 30 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 1: CACAATGCAT CCCCTTTATC CGCCTGCCGT 30 (2) INFORMATION FOR SEQ ID NO: 2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2: CAATTGCGAC TTGGAGGACA TGATGGGCAG ATGAGGG 37 (2) INFORMATION FOR SEQ ID NO: 3: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 3: AGAGAGGATA TCGATGTGGG 20 (2) INFORMATION FOR SEQ ID NO: 4: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4: CCCTCATCTG CCCATCATGT CCTCCAAGTC GCAATTG 37 (2) INFORMATION FOR SEQ ID NO: 5: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2054 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iii) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Aspergillus tubigensis (ix) FEATURE: (A) NAME/KEY: TATA_signal (B) LOCATION: 848..854 (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 950..1179 (ix) FEATURE: (A) NAME/KEY: intron (B) LOCATION: 1179..1228 (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 1229..1631 (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: join(950..1179, 1229..1631) (D) OTHER INFORMATION: /EC_number= 3.2.1.8. /product= “1,4-beta-xylanxylanohydrolase” /gene= “xlnA” /standard_name= “endo-xylanase” (ix) FEATURE: (A) NAME/KEY: mat_peptide (B) LOCATION: 1031..1631 (ix) FEATURE: (A) NAME/KEY: sig_peptide (B) LOCATION: 950..1031 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 5: AACGTCTGCA GTCCCGTACT GTTTACCAAA ATGCCAGGCC ACTGGTGGAT ATACAACTTT 60 GTAATACGTT GCCGGAGTCA GCCCCTACTC CCTGATGGGT TCCCACTCCC TAGTTACTTC 120 CTACTGGGTA GTAGGCTCCT AGAGTGGGGT AAAGTTTGCC AAGGGTTTAG CCCCAGTCTT 180 GTTTATGCTT GGCTAGGCAG GACCTGGGTA AGTTGATGGC TCCTGCATTC CTACCTGAGT 240 ATTTCCAGCT ATAAGCGAGA TTTGCCATAC TCTTCAGCGA GTCCGGATGG TCCGCGCCGA 300 GGTTGACCCT GCCTTCATCA CCTACACAAA GAACTCCTCG GCCAACTCCC GGTGGCCTTC 360 GAGCTCCAAA GTACCTTCGC GACCTTTGGC CAGTGTTTCT CGCAGCGTTT ACTGAGCCTA 420 AGGCTTGCTA CAATAAATAA AGAGACATAA CCTTGCAGTA CATACGTCTT GTATGAGCGA 480 GGAACTGTGT TCAGTAGTAG ATCAGTGGGT ACATAATCAT GAACATGACT TCTGAGCCAG 540 AAAACCTTCT GCAGGGAACC GGTGAAGAAA CCCCACTTCC CCGCCTCCAC TAACTGCAGC 600 CCCTTTATCC GCCTGCCGTC CATTTAGCCA AATGTAGTCC ATTTAGCCAA GTGCGGTCCA 660 TTTAGCCAAG TCCAGTGCTT AGGTTGGTGG CTACACAGGA AACGGCCATG AATGTAGACA 720 CAACTATAGA ACTGTCCCTA GAAATAGGCT CGAGGTTGTT AGAGCGTTTA AGGTGATGCG 780 GCAAAATGCA TATGACTGAG TTGCTTCAAC GTGCAGGGGA AAGGGATAAA TAGTCTTTTT 840 CGCAGAATAT AAATAGAGGT AGAGCGGGCT CGCAGCAATA TTGACCAGGA CAGGGCTTCT 900 TTTCCAGTTG CATACATCCA TTCACAGCAT TCAGCTTTCT TCAATCATC ATG AAG 955 Met Lys -27 GTC ACT GCG GCT TTT GCA GGT CTT TTG GTC ACG GCA TTC GCC GCT CCT 1003 Val Thr Ala Ala Phe Ala Gly Leu Leu Val Thr Ala Phe Ala Ala Pro -25 -20 -15 -10 GCC CCA GAA CCT GAT CTG GTG TCG CGA AGT GCC GGT ATC AAC TAC GTG 1051 Ala Pro Glu Pro Asp Leu Val Ser Arg Ser Ala Gly Ile Asn Tyr Val -5 1 5 CAA AAC TAC AAC GGC AAC CTT GGT GAT TTC ACC TAC GAC GAG AGT GCC 1099 Gln Asn Tyr Asn Gly Asn Leu Gly Asp Phe Thr Tyr Asp Glu Ser Ala 10 15 20 GGA ACA TTT TCC ATG TAC TGG GAA GAT GGA GTG AGC TCC GAC TTT GTC 1147 Gly Thr Phe Ser Met Tyr Trp Glu Asp Gly Val Ser Ser Asp Phe Val 25 30 35 GTT GGT CTG GGC TGG ACC ACT GGT TCT TCT AA GTGAGTGACT 1189 Val Gly Leu Gly Trp Thr Thr Gly Ser Ser Asn 40 45 50 GTATTCTTTA ACCAAGGTCT AGGATCTAAC GTCTTTCAG C GCT ATC ACC TAC TCT 1244 Ala Ile Thr Tyr Ser 55 GCC GAA TAC AGC GCT TCT GGC TCC GCT TCC TAC CTC GCT GTG TAC GGC 1292 Ala Glu Tyr Ser Ala Ser Gly Ser Ala Ser Tyr Leu Ala Val Tyr Gly 60 65 70 TGG GTC AAC TAT CCT CAA GCT GAG TAC TAC ATC GTC GAG GAT TAC GGT 1340 Trp Val Asn Tyr Pro Gln Ala Glu Tyr Tyr Ile Val Glu Asp Tyr Gly 75 80 85 GAT TAT AAC CCT TGC AGT TCG GCC ACA AGC CTT GGT ACC GTG TAC TCT 1388 Asp Tyr Asn Pro Cys Ser Ser Ala Thr Ser Leu Gly Thr Val Tyr Ser 90 95 100 GAT GGA AGC ACC TAC CAA GTC TGC ACC GAC ACT CGA ACA AAC GAA CCG 1436 Asp Gly Ser Thr Tyr Gln Val Cys Thr Asp Thr Arg Thr Asn Glu Pro 105 110 115 TCC ATC ACG GGA ACA AGC ACG TTC ACG CAG TAC TTC TCC GTT CGA GAG 1484 Ser Ile Thr Gly Thr Ser Thr Phe Thr Gln Tyr Phe Ser Val Arg Glu 120 125 130 135 AGC ACG CGC ACA TCT GGA ACG GTG ACT GTT GCC AAC CAT TTC AAC TTC 1532 Ser Thr Arg Thr Ser Gly Thr Val Thr Val Ala Asn His Phe Asn Phe 140 145 150 TGG GCG CAC CAT GGG TTC GGC AAT AGC GAC TTC AAT TAT CAG GTC GTG 1580 Trp Ala His His Gly Phe Gly Asn Ser Asp Phe Asn Tyr Gln Val Val 155 160 165 GCG GTG GAA GCA TGG AGC GGT GCT GGC AGC GCT AGT GTC ACA ATC TCT 1628 Ala Val Glu Ala Trp Ser Gly Ala Gly Ser Ala Ser Val Thr Ile Ser 170 175 180 TCT TGAGAGATTA GTGCCCTAGT AGTCGGAAGA TATCAACGCG GCAGTTTGCT 1681 Ser CTCAGGTGGT GTGATGATCG GATCCGGTCT CTGGGGTTAC ATTGAGGCTG TATAAGTTGT 1741 TGTGGGGCCG AGCTGTCAGC GGCTGCGTTT TCAGCTTGCA CAGATAATCA ACTCTCGTTT 1801 TCTATCTCTT GCGTTTCCTC GCTGCTTATC CTATCCATAG ATAATTATTT TGCCCACTAC 1861 CACAACTTGT TCGGTCGCAG TAGTCACTCC GAGCAAGGCA TTGGGAAATG GGGGATGCGG 1921 GGTGCTGCGT ACCCTCTAAC CTAGGGCATT TTAAAGGATA TTTACCCTCC AGATATTCTA 1981 TAGATACAGA CTTCTTAGGA CTGCGGGTAA TATAGAGAGC GAAATTTCTA CAGTTCGATG 2041 CAGTTCAATG CGA 2054 (2) INFORMATION FOR SEQ ID NO: 6: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 3026 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iii) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Aspergillus niger (B) STRAIN: N400 (CBS 120.49) (ix) FEATURE: (A) NAME/KEY: TATA_signal (B) LOCATION: 643..648 (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 724..2538 (D) OTHER INFORMATION: /EC_number= 1.1.3.4. /product= “glucose oxidase” /gene= “goxC” (ix) FEATURE: (A) NAME/KEY: mat_peptide (B) LOCATION: 790..2538 (ix) FEATURE: (A) NAME/KEY: sig_peptide (B) LOCATION: 724..790 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 6: CTGCAGGTAC CTGAAGCCTG CCTAGTTTGA TCACCCTGAA ACCAGCACTG CCTGTCTTGA 60 CCTTGGTGGT GAGTTTGCAC GTGGGCTGGC TGTTCAAATA AACTCTCCAA TTGACCCTCT 120 CCCCGTGGAG AACACAGCAA ACACTATAGG CTTTCCATTG AGGGCATGAC GAGGACCCTA 180 TGGTTTGTGC ACTTGGCGAG GGCTGACCGG AGCACGAATC GGGAAGGGCA GAACTCAGAA 240 TTCGGTGTTC TCGGCATGCC GAAAGTCGGT ATCCCTTGGC GCCACGATGA TTTGCGTCCA 300 GGATTCGTAT AGTTCCTCGT CCACGAGGCT GCCTACCGTC AGCGTGAGGC AGTGAGCTAA 360 TATGGGGCCA ATAAGCCACT ACGAGGATGA CATGGCCTCT ACAGAACGAG AGACGCAGAG 420 GATCAGGACG CCAATCCTGC GCTCCACCTG TCTAAGGATT CGCTTTTGGA CTATCCAGGG 480 ATTATGGCTT CGGATTATTG TATTCGGGAT ACCGACGGCT GAGCACACGG AGGATGAGGT 540 TCAGCTCACG GCCCCTATCA GTATGCATTA TGAGGATGGC TTCTTGGAAA GCAGAGGAAT 600 TGGATTATCG AACAAGTTGG TTCTGGACCA TTGACTCGAG CGTATAAGTA ACCTCGTTCG 660 GTCCTCCTGT CACCTTCTGA TCAGCAACCA GCCTTTCCTC TCTCATTCCC TCATCTGCCC 720 ATC ATG CAG ACT CTC CTT GTG AGC TCG CTT GTG GTC TCC CTC GCT GCG 768 Met Gln Thr Leu Leu Val Ser Ser Leu Val Val Ser Leu Ala Ala -22 -20 -15 -10 GCC CTG CCA CAC TAC ATC AGG AGC AAT GGC ATT GAA GCC AGC CTC CTG 816 Ala Leu Pro His Tyr Ile Arg Ser Asn Gly Ile Glu Ala Ser Leu Leu -5 1 5 ACT GAT CCC AAG GAT GTC TCC GGC CGC ACG GTC GAC TAC ATC ATC GCT 864 Thr Asp Pro Lys Asp Val Ser Gly Arg Thr Val Asp Tyr Ile Ile Ala 10 15 20 25 GGT GGA GGT CTG ACT GGA CTC ACC ACC GCT GCT CGT CTG ACG GAG AAC 912 Gly Gly Gly Leu Thr Gly Leu Thr Thr Ala Ala Arg Leu Thr Glu Asn 30 35 40 CCC AAC ATC AGT GTG CTC GTC ATC GAA AGT GGC TCC TAC GAG TCG GAC 960 Pro Asn Ile Ser Val Leu Val Ile Glu Ser Gly Ser Tyr Glu Ser Asp 45 50 55 AGA GGT CCT ATC ATT GAG GAC CTG AAC GCC TAC GGC GAC ATC TTT GGC 1008 Arg Gly Pro Ile Ile Glu Asp Leu Asn Ala Tyr Gly Asp Ile Phe Gly 60 65 70 AGC AGT GTA GAC CAC GCC TAC GAG ACC GTG GAG CTC GCT ACC AAC AAT 1056 Ser Ser Val Asp His Ala Tyr Glu Thr Val Glu Leu Ala Thr Asn Asn 75 80 85 CAA ACC GCG CTG ATC CGC TCC GGA AAT GGT CTC GGT GGC TCT ACT CTA 1104 Gln Thr Ala Leu Ile Arg Ser Gly Asn Gly Leu Gly Gly Ser Thr Leu 90 95 100 105 GTG AAT GGT GGC ACC TGG ACT CGC CCC CAC AAG GCA CAG GTT GAC TCT 1152 Val Asn Gly Gly Thr Trp Thr Arg Pro His Lys Ala Gln Val Asp Ser 110 115 120 TGG GAG ACT GTC TTT GGA AAT GAG GGC TGG AAC TGG GAC AAT GTG GCC 1200 Trp Glu Thr Val Phe Gly Asn Glu Gly Trp Asn Trp Asp Asn Val Ala 125 130 135 GCC TAC TCC CTC CAG GCT GAG CGT GCT CGC GCA CCA AAT GCC AAA CAG 1248 Ala Tyr Ser Leu Gln Ala Glu Arg Ala Arg Ala Pro Asn Ala Lys Gln 140 145 150 ATC GCT GCT GGC CAC TAC TTC AAC GCA TCC TGC CAT GGT GTT AAT GGT 1296 Ile Ala Ala Gly His Tyr Phe Asn Ala Ser Cys His Gly Val Asn Gly 155 160 165 ACT GTC CAT GCC GGA CCC CGC GAC ACC GGC GAT GAC TAT TCT CCC ATC 1344 Thr Val His Ala Gly Pro Arg Asp Thr Gly Asp Asp Tyr Ser Pro Ile 170 175 180 185 GTC AAG GCT CTC ATG AGC GCT GTC GAA GAC CGG GGC GTT CCC ACC AAG 1392 Val Lys Ala Leu Met Ser Ala Val Glu Asp Arg Gly Val Pro Thr Lys 190 195 200 AAA GAC TTC GGA TGC GGT GAC CCC CAT GGT GTG TCC ATG TTC CCC AAC 1440 Lys Asp Phe Gly Cys Gly Asp Pro His Gly Val Ser Met Phe Pro Asn 205 210 215 ACC TTG CAC GAA GAC CAA GTG CGC TCC GAT GCC GCT CGC GAA TGG CTA 1488 Thr Leu His Glu Asp Gln Val Arg Ser Asp Ala Ala Arg Glu Trp Leu 220 225 230 CTT CCC AAC TAC CAA CGT CCC AAC CTG CAA GTC CTG ACC GGA CAG TAT 1536 Leu Pro Asn Tyr Gln Arg Pro Asn Leu Gln Val Leu Thr Gly Gln Tyr 235 240 245 GTT GGT AAG GTG CTC CTT AGC CAG AAC GGC ACC ACC CCT CGT GCC GTT 1584 Val Gly Lys Val Leu Leu Ser Gln Asn Gly Thr Thr Pro Arg Ala Val 250 255 260 265 GGC GTG GAA TTC GGC ACC CAC AAG GGC AAC ACC CAC AAC GTT TAC GCT 1632 Gly Val Glu Phe Gly Thr His Lys Gly Asn Thr His Asn Val Tyr Ala 270 275 280 AAG CAC GAG GTC CTC CTG GCC GCG GGC TCC GCT GTC TCT CCC ACA ATC 1680 Lys His Glu Val Leu Leu Ala Ala Gly Ser Ala Val Ser Pro Thr Ile 285 290 295 CTC GAA TAT TCC GGT ATC GGA ATG AAG TCC ATC CTG GAG CCC CTT GGT 1728 Leu Glu Tyr Ser Gly Ile Gly Met Lys Ser Ile Leu Glu Pro Leu Gly 300 305 310 ATC GAC ACC GTC GTT GAC CTG CCC GTC GGC TTG AAC CTG CAG GAC CAG 1776 Ile Asp Thr Val Val Asp Leu Pro Val Gly Leu Asn Leu Gln Asp Gln 315 320 325 ACC ACC GCT ACC GTC CGC TCC CGC ATC ACC TCT GCT GGT GCA GGA CAG 1824 Thr Thr Ala Thr Val Arg Ser Arg Ile Thr Ser Ala Gly Ala Gly Gln 330 335 340 345 GGA CAG GCC GCT TGG TTC GCC ACC TTC AAC GAG ACC TTT GGT GAC TAT 1872 Gly Gln Ala Ala Trp Phe Ala Thr Phe Asn Glu Thr Phe Gly Asp Tyr 350 355 360 TCC GAA AAG GCA CAC GAG CTG CTC AAC ACC AAG CTG GAG CAG TGG GCC 1920 Ser Glu Lys Ala His Glu Leu Leu Asn Thr Lys Leu Glu Gln Trp Ala 365 370 375 GAA GAG GCC GTC GCC CGT GGC GGA TTC CAC AAC ACC ACC GCC TTG CTC 1968 Glu Glu Ala Val Ala Arg Gly Gly Phe His Asn Thr Thr Ala Leu Leu 380 385 390 ATC CAG TAC GAG AAC TAC CGC GAC TGG ATT GTC AAC CAC AAC GTC GCG 2016 Ile Gln Tyr Glu Asn Tyr Arg Asp Trp Ile Val Asn His Asn Val Ala 395 400 405 TAC TCG GAA CTC TTC CTC GAC ACT GCC GGA GTA GCC AGC TTC GAT GTG 2064 Tyr Ser Glu Leu Phe Leu Asp Thr Ala Gly Val Ala Ser Phe Asp Val 410 415 420 425 TGG GAC CTT CTG CCC TTC ACC CGA GGA TAC GTT CAC ATC CTC GAC AAG 2112 Trp Asp Leu Leu Pro Phe Thr Arg Gly Tyr Val His Ile Leu Asp Lys 430 435 440 GAC CCC TAC CTT CAC CAC TTC GCC TAC GAC CCT CAG TAC TTC CTC AAC 2160 Asp Pro Tyr Leu His His Phe Ala Tyr Asp Pro Gln Tyr Phe Leu Asn 445 450 455 GAG CTG GAC CTG CTC GGT CAG GCT GCC GCT ACT CAA CTG GCC CGC AAC 2208 Glu Leu Asp Leu Leu Gly Gln Ala Ala Ala Thr Gln Leu Ala Arg Asn 460 465 470 ATC TCC AAC TCC GGT GCC ATG CAG ACC TAC TTC GCT GGG GAG ACT ATC 2256 Ile Ser Asn Ser Gly Ala Met Gln Thr Tyr Phe Ala Gly Glu Thr Ile 475 480 485 CCC GGT GAT AAC CTC GCG TAT GAT GCC GAT TTG AGC GCC TGG ACT GAG 2304 Pro Gly Asp Asn Leu Ala Tyr Asp Ala Asp Leu Ser Ala Trp Thr Glu 490 495 500 505 TAC ATC CCG TAC CAC TTC CGT CCT AAC TAC CAT GGC GTG GGT ACT TGC 2352 Tyr Ile Pro Tyr His Phe Arg Pro Asn Tyr His Gly Val Gly Thr Cys 510 515 520 TCC ATG ATG CCG AAG GAG ATG GGC GGT GTT GTT GAT AAT GCT GCC CGT 2400 Ser Met Met Pro Lys Glu Met Gly Gly Val Val Asp Asn Ala Ala Arg 525 530 535 GTG TAT GGT GTG CAG GGA CTG CGT GTC ATT GAT GGT TCT ATT CCT CCT 2448 Val Tyr Gly Val Gln Gly Leu Arg Val Ile Asp Gly Ser Ile Pro Pro 540 545 550 ACG CAA ATG TCG TCC CAT GTC ATG ACG GTG TTC TAT GCC ATG GCG CTA 2496 Thr Gln Met Ser Ser His Val Met Thr Val Phe Tyr Ala Met Ala Leu 555 560 565 AAA ATT TCG GAT GCT ATC TTG GAA GAT TAT GCT TCC ATG CAG 2538 Lys Ile Ser Asp Ala Ile Leu Glu Asp Tyr Ala Ser Met Gln 570 575 580 TGAGTGGTAT GATGGGGATA TGAGTGAGGA TATTAGGGGA TGGTACTTAG ATGCTGGGGA 2598 GGTATAATCA TAGATTGGAT AGAATTGGTA GGTTACATAG ACAGGTTACA TGAATAGACG 2658 TTCGTTATAT GTGAGCAGAC ATTACTACCA AACAAGGGCA TTGTTCAGTT AGTCGAACGA 2718 TAGTCATATG TTTTGTACGG GAAGAAAGTT TCACTAATTA TTAAGCAAAC GGATCAGGGG 2778 TTGCCAGCTA AAATACAATC ATCCGATGTT CTATTTTCTT CAAATTGATC GACCAGTCAG 2838 TTAATGAATG CATGAGAGCA ACTCTGCGCA TCCTCTAGCT ATCTAGTCAA TAATAAGCAT 2898 GTTGTTTAAG ATGAAACACC GCCATAGACA TATTCTGTTG CTGGTGAAGC AAGCCCTCGC 2958 TAAATATGCT GATAACTTCC TATGCCAGTA GAATATTTTC CCACTCTGCT GCGCGCTCTC 3018 AAAAGCTT 3026 (2) INFORMATION FOR SEQ ID NO: 7: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1517 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Aspergillus niger (B) STRAIN: L112 (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 339..495 (ix) FEATURE: (A) NAME/KEY: intron (B) LOCATION: 496..563 (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 564..1237 (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: join(339..495, 564..1237) (D) OTHER INFORMATION: /product= “orotidine-5′-phosphate decarboxylase” (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7: GCAGGGAAAA ATACGAGCTC CAATGAACCT GGGTGTGGCA ACTTCAATGG AAAGGAACTG 60 CCTTTGCAGG TGTGGCTGAA CCCCACGGTT CCGGTCGGAG GCGGCGAAAT CACCCGATGT 120 GGCTGGTGCG TGGAGGGTCG CGATGATTTA CTGAGCTCCT CTTTTGCTCG ACATTGAATG 180 TGCATTGTTC ACCTCATATA AGGGCCAGTC GCTGCTAAAT TATTCGGTAG TATTTGCGCA 240 TCTCTGGATC TACCAATTAG GGCCTATCAG TCGAAACTCC AAGCTACTCA TATTGCACAA 300 GCCTCTTTCA TCCCCGCATT AACCCCTCCA CCGACACC ATG TCC TCC AAG TCG 353 Met Ser Ser Lys Ser 1 5 CAA TTG ACC TAC ACT GCC CGT GCC AGC AAG CAC CCC AAT GCT CTG GCC 401 Gln Leu Thr Tyr Thr Ala Arg Ala Ser Lys His Pro Asn Ala Leu Ala 10 15 20 AAG CGG CTG TTC GAA ATT GCT GAG GCC AAG AAG ACC AAT GTG ACC GTC 449 Lys Arg Leu Phe Glu Ile Ala Glu Ala Lys Lys Thr Asn Val Thr Val 25 30 35 TCT GCC GAC GTT ACC ACC ACT AAG GAG CTA CTA GAT CTT GCT GAC C 495 Ser Ala Asp Val Thr Thr Thr Lys Glu Leu Leu Asp Leu Ala Asp 40 45 50 GTAGGCCGAC CCGCCATTCT GCCTGTTTAT GCTGCATACA AACTTATTAA CGGTGATACC 555 GGACTGAG GT CTC GGT CCC TAC ATC GCC GTG ATC AAA ACC CAC ATC GAT 604 Arg Leu Gly Pro Tyr Ile Ala Val Ile Lys Thr His Ile Asp 55 60 65 ATC CTC TCT GAC TTC AGC GAC GAG ACC ATT GAG GGC CTC AAG GCT CTT 652 Ile Leu Ser Asp Phe Ser Asp Glu Thr Ile Glu Gly Leu Lys Ala Leu 70 75 80 GCG CAG AAG CAC AAC TTC CTC ATC TTC GAG GAC CGC AAA TTC ATC GAC 700 Ala Gln Lys His Asn Phe Leu Ile Phe Glu Asp Arg Lys Phe Ile Asp 85 90 95 ATT GGC AAC ACT GTC CAG AAG CAA TAC CAC CGT GGT ACC CTC CGC ATC 748 Ile Gly Asn Thr Val Gln Lys Gln Tyr His Arg Gly Thr Leu Arg Ile 100 105 110 TCA GAA TGG GCC CAT ATC ATC AAC TGC AGC ATC CTG CCT GGC GAG GGT 796 Ser Glu Trp Ala His Ile Ile Asn Cys Ser Ile Leu Pro Gly Glu Gly 115 120 125 130 ATC GTC GAG GCT CTC GCT CAG ACG GCG TCT GCA CCG GAC TTC TCC TAC 844 Ile Val Glu Ala Leu Ala Gln Thr Ala Ser Ala Pro Asp Phe Ser Tyr 135 140 145 GGC CCC GAA CGT GGT CTG TTG ATC TTG GCG GAA ATG ACC TCT AAG GGT 892 Gly Pro Glu Arg Gly Leu Leu Ile Leu Ala Glu Met Thr Ser Lys Gly 150 155 160 TCC TTG GCC ACC GGC CAG TAC ACT ACT TCT TCG GTT GAT TAT GCC CGG 940 Ser Leu Ala Thr Gly Gln Tyr Thr Thr Ser Ser Val Asp Tyr Ala Arg 165 170 175 AAA TAC AAG AAC TTC GTC ATG GGA TTT GTG TCG ACC CGC TCG TTG GGT 988 Lys Tyr Lys Asn Phe Val Met Gly Phe Val Ser Thr Arg Ser Leu Gly 180 185 190 GAG GTG CAG TCG GAA GTC AGC TCT CCT TCG GAT GAG GAG GAC TTT GTG 1036 Glu Val Gln Ser Glu Val Ser Ser Pro Ser Asp Glu Glu Asp Phe Val 195 200 205 210 GTC TTC ACG ACT GGT GTG AAC ATT TCG TCC AAG GGA GAT AAG CTC GGT 1084 Val Phe Thr Thr Gly Val Asn Ile Ser Ser Lys Gly Asp Lys Leu Gly 215 220 225 CAG CAG TAC CAG ACT CCC GCA TCG GCT ATC GGT CGG GGT GCT GAC TTC 1132 Gln Gln Tyr Gln Thr Pro Ala Ser Ala Ile Gly Arg Gly Ala Asp Phe 230 235 240 ATT ATC GCG GGT CGC GGT ATC TAC GCC GCG CCG GAC CCG GTG CAG GCT 1180 Ile Ile Ala Gly Arg Gly Ile Tyr Ala Ala Pro Asp Pro Val Gln Ala 245 250 255 GCG CAA CAG TAC CAG AAG GAA GGT TGG GAG GCG TAC CTG GCC CGT GTC 1228 Ala Gln Gln Tyr Gln Lys Glu Gly Trp Glu Ala Tyr Leu Ala Arg Val 260 265 270 GGC GGA AAC TAATACTATA AAATGAGGAA AAAAGTTTTG ATGGTTATGA 1277 Gly Gly Asn 275 ATGATATAGA AATGCAACTT GCCGCTACGA TACGCATACA AACTAATGTC GAGCACGGGT 1337 AGTCAGACTG CGGCATCGGA TGTCAAAACG GTATTGATCC TGCAGGCTAT TATAGGGTGG 1397 CACGGGATTA ATGCGGTACG ACGATTTGAT GCAGATAAGC AGGCTGCGAA GTACTTAGTC 1457 CTGTAACTCT TGCGTAGAGC AAATGGCGAC GGGTGGCTGA TAAGGGACGG TGATAAGCTT 1517 (2) INFORMATION FOR SEQ ID NO: 8: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 4108 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iii) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Aspergillus niger (CBS 120.49) (B) STRAIN: NW147 (ix) FEATURE: (A) NAME/KEY: TATA_signal (B) LOCATION: 787..794 (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 855..3266 (D) OTHER INFORMATION: /EC_number= 3.2.1.37 /product= “1,4-beta-D-xylan xylanohydrolase” /gene= “xlnD” /standard_name= “beta-xylosidase” (ix) FEATURE: (A) NAME/KEY: sig_peptide (B) LOCATION: 855..932 (ix) FEATURE: (A) NAME/KEY: mat_peptide (B) LOCATION: 933..3266 (ix) FEATURE: (A) NAME/KEY: polyA_site (B) LOCATION: 3383 (ix) FEATURE: (A) NAME/KEY: polyA_site (B) LOCATION: 3404 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8: CTGCAGGCCA TGTATCCTGC GAAGATGGGT GAGTGGAAGA AAATCGTCAA GATTGAGGCG 60 GAGATGGCGA GGGCCGCGAT GAAGAAGGGT GGCTGGGCAC CGGAGAAGCC AGCCACCGCC 120 ACGGCGGCGC AGATGAGTAT ACCGTATGCG GTGGCGTTGC AGGTTCTGGA TGGGGAGATT 180 GTGCCGGGGC AGTTTGCGCC GGGCATGTTG AATCGGGAGG AGTTATGGGA TGTGATTAGG 240 CTGGTGGAAT GTCGGGAGGC CAAGGAGCTG GATAATACGT GGGCGCAGAG GGTCAAGATC 300 ACGTTTGAGG ATGGGGAGGT GGTGGAGAAG TTGTTGAAGG CTCCGAAGGG AGTCCATCCT 360 GGGGTGACGA ATGAGGAGGT GTTGCAGAAG TGGCGGGCTG TGACGAAGGG GGTAATTTCG 420 GAAGAGAGGC AGAAGAAGAT CGAGGAGATT GTGTTGAATT TGGAAGAGGT GGAGGATGTG 480 GCTGGTGTTT TGGGCGAGTT GTTGAGGGAA GAGACGGTGA ATGTGCTGCA GTAGACGGTT 540 ACCCCATTTG GACGGGGATG GCTTCATATT TCCCAAGCGA TGTCACGCCA TAGAAAGGGC 600 ACATTTACCC GGTGCCTGAG CGAAACTCTA CTTCGAAGAC AATGCCAATG TTTAACTATC 660 TTGTTTTAAT TGCTAAATGC AAACATTCCA GGTTCTTCCT AATGCCGGCT AAATCATTCA 720 GGCTAAACCC CCGCGATGAA GTCAATCGGT CATTCTCCGG CGCATCTCCG CATCTCCGCA 780 AACCGCTATA AAATCTACCC CAGATTCAGT CCCCGGCCAC CTTTCTATCC CCCCCCCCAC 840 AGACTGGCTC AACC ATG GCG CAC TCA ATG TCT CGT CCC GTG GCT GCC ACT 890 Met Ala His Ser Met Ser Arg Pro Val Ala Ala Thr -26 -25 -20 -15 GCC GCT GCT CTG CTG GCT CTG GCT CTT CCT CAA GCT CTT GCC CAG GCC 938 Ala Ala Ala Leu Leu Ala Leu Ala Leu Pro Gln Ala Leu Ala Gln Ala -10 -5 1 AAC ACC AGC TAC GTC GAC TAC AAC ATC GAA GCC AAC CCG GAC TTG TAT 986 Asn Thr Ser Tyr Val Asp Tyr Asn Ile Glu Ala Asn Pro Asp Leu Tyr 5 10 15 CCT TTG TGC ATA GAA ACC ATC CCA CTG AGC TTC CCC GAC TGC CAG AAT 1034 Pro Leu Cys Ile Glu Thr Ile Pro Leu Ser Phe Pro Asp Cys Gln Asn 20 25 30 GGT CCC CTG CGC AGC CAT CTC ATC TGT GAT GAA ACA GCC ACC CCC TAT 1082 Gly Pro Leu Arg Ser His Leu Ile Cys Asp Glu Thr Ala Thr Pro Tyr 35 40 45 50 GAC CGA GCA GCA TCG CTC ATC TCG CTC TTC ACC CTG GAC GAG CTG ATC 1130 Asp Arg Ala Ala Ser Leu Ile Ser Leu Phe Thr Leu Asp Glu Leu Ile 55 60 65 GCC AAC ACC GGC AAC ACC GGC CTC GGT GTC TCC CGA CTG GGC CTC CCT 1178 Ala Asn Thr Gly Asn Thr Gly Leu Gly Val Ser Arg Leu Gly Leu Pro 70 75 80 GCA TAC CAA GTA TGG AGT GAA GCT CTT CAC GGC CTC GAC CGT GCC AAT 1226 Ala Tyr Gln Val Trp Ser Glu Ala Leu His Gly Leu Asp Arg Ala Asn 85 90 95 TTC AGC GAC TCA GGA GCC TAC AAT TGG GCC ACC TCA TTC CCC CAG CCC 1274 Phe Ser Asp Ser Gly Ala Tyr Asn Trp Ala Thr Ser Phe Pro Gln Pro 100 105 110 ATC CTG ACC ACC GCG GCC CTC AAC CGC ACC CTC ATC CAC CAA ATC GCC 1322 Ile Leu Thr Thr Ala Ala Leu Asn Arg Thr Leu Ile His Gln Ile Ala 115 120 125 130 TCC ATC ATC TCT ACC CAA GGC CGC GCC TTC AAC AAC GCC GGC CGC TAC 1370 Ser Ile Ile Ser Thr Gln Gly Arg Ala Phe Asn Asn Ala Gly Arg Tyr 135 140 145 GGC CTC GAC GTC TAC GCC CCC AAC ATC AAC ACC TTC CGC CAC CCC GTC 1418 Gly Leu Asp Val Tyr Ala Pro Asn Ile Asn Thr Phe Arg His Pro Val 150 155 160 TGG GGT CGC GGA CAA GAA ACC CCA GGA GAG GAC GTC TCT CTC GCC GCC 1466 Trp Gly Arg Gly Gln Glu Thr Pro Gly Glu Asp Val Ser Leu Ala Ala 165 170 175 GTC TAC GCC TAC GAA TAC ATC ACC GGC ATC CAG GGT CCC GAC CCA GAA 1514 Val Tyr Ala Tyr Glu Tyr Ile Thr Gly Ile Gln Gly Pro Asp Pro Glu 180 185 190 TCA AAC CTC AAA CTC GCC GCC ACG GCC AAG CAC TAC GCC GGC TAT GAC 1562 Ser Asn Leu Lys Leu Ala Ala Thr Ala Lys His Tyr Ala Gly Tyr Asp 195 200 205 210 ATC GAG AAC TGG CAC AAC CAC TCC CGC CTG GGC AAC GAC ATG AAC ATC 1610 Ile Glu Asn Trp His Asn His Ser Arg Leu Gly Asn Asp Met Asn Ile 215 220 225 ACC CAG CAA GAC CTC TCC GAA TAC TAC ACG CCC CAA TTC CAC GTC GCC 1658 Thr Gln Gln Asp Leu Ser Glu Tyr Tyr Thr Pro Gln Phe His Val Ala 230 235 240 GCC CGC GAC GCC AAA GTC CAG AGT GTC ATG TGC GCC TAC AAC GCC GTC 1706 Ala Arg Asp Ala Lys Val Gln Ser Val Met Cys Ala Tyr Asn Ala Val 245 250 255 AAC GGC GTC CCT GCC TGC GCC GAC TCC TAC TTC CTC CAG ACC CTC CTC 1754 Asn Gly Val Pro Ala Cys Ala Asp Ser Tyr Phe Leu Gln Thr Leu Leu 260 265 270 CGC GAC ACC TTC GGA TTT GTC GAC CAC GGA TAC GTC TCC AGC GAC TGC 1802 Arg Asp Thr Phe Gly Phe Val Asp His Gly Tyr Val Ser Ser Asp Cys 275 280 285 290 GAT GCC GCC TAT AAC ATC TAC AAC CCC CAC GGC TAT GCC TCC TCC CAG 1850 Asp Ala Ala Tyr Asn Ile Tyr Asn Pro His Gly Tyr Ala Ser Ser Gln 295 300 305 GCT GCC GCT GCC GCT GAG GCC ATC CTC GCC GGC ACC GAC ATC GAC TGC 1898 Ala Ala Ala Ala Ala Glu Ala Ile Leu Ala Gly Thr Asp Ile Asp Cys 310 315 320 GGT ACC ACC TAC CAA TGG CAC CTG AAC GAG TCC ATC GCT GCG GGA GAT 1946 Gly Thr Thr Tyr Gln Trp His Leu Asn Glu Ser Ile Ala Ala Gly Asp 325 330 335 CTC TCT CGC GAT GAT ATT GAG CAG GGT GTG ATT CGT CTC TAC ACG ACC 1994 Leu Ser Arg Asp Asp Ile Glu Gln Gly Val Ile Arg Leu Tyr Thr Thr 340 345 350 CTC GTG CAG GCC GGA TAC TTC GAC TCC AAC ACC ACA AAG GCG AAC AAC 2042 Leu Val Gln Ala Gly Tyr Phe Asp Ser Asn Thr Thr Lys Ala Asn Asn 355 360 365 370 CCC TAC CGC GAC CTC TCC TGG TCC GAC GTC CTT GAG ACG GAC GCA TGG 2090 Pro Tyr Arg Asp Leu Ser Trp Ser Asp Val Leu Glu Thr Asp Ala Trp 375 380 385 AAC ATC TCC TAC CAA GCC GCG ACG CAG GGC ATT GTC CTT CTC AAG AAC 2138 Asn Ile Ser Tyr Gln Ala Ala Thr Gln Gly Ile Val Leu Leu Lys Asn 390 395 400 TCC AAC AAC GTC CTC CCC CTC ACC GAG AAA GCT TAC CCA CCA TCC AAC 2186 Ser Asn Asn Val Leu Pro Leu Thr Glu Lys Ala Tyr Pro Pro Ser Asn 405 410 415 ACC ACC GTC GCC CTC ATC GGT CCC TGG GCC AAC GCC ACC ACC CAA CTC 2234 Thr Thr Val Ala Leu Ile Gly Pro Trp Ala Asn Ala Thr Thr Gln Leu 420 425 430 CTG GGC AAC TAC TAC GGC AAC GCT CCC TAC ATG ATC AGC CCC CGC GCC 2282 Leu Gly Asn Tyr Tyr Gly Asn Ala Pro Tyr Met Ile Ser Pro Arg Ala 435 440 445 450 GCC TTC GAA GAA GCC GGA TAC AAA GTC AAC TTC GCC GAG GGC ACC GGT 2330 Ala Phe Glu Glu Ala Gly Tyr Lys Val Asn Phe Ala Glu Gly Thr Gly 455 460 465 ATC TCC TCC ACA AGC ACC TCG GGC TTC GCT GCC GCC TTA TCC GCC GCA 2378 Ile Ser Ser Thr Ser Thr Ser Gly Phe Ala Ala Ala Leu Ser Ala Ala 470 475 480 CAA TCC GCC GAC GTG ATA ATC TAC GCC GGT GGT ATC GAC AAT ACC CTT 2426 Gln Ser Ala Asp Val Ile Ile Tyr Ala Gly Gly Ile Asp Asn Thr Leu 485 490 495 GAA GCG GAG GCA CTG GAT CGA GAG AGT ATC GCG TGG CCG GGT AAC CAA 2474 Glu Ala Glu Ala Leu Asp Arg Glu Ser Ile Ala Trp Pro Gly Asn Gln 500 505 510 CTG GAC TTG ATC CAG AAG CTC GCC TCG GCG GCC GGA AAG AAG CCG CTC 2522 Leu Asp Leu Ile Gln Lys Leu Ala Ser Ala Ala Gly Lys Lys Pro Leu 515 520 525 530 ATC GTC CTC CAA ATG GGC GGC GGA CAG GTC GAT TCC TCT TCG CTC AAG 2570 Ile Val Leu Gln Met Gly Gly Gly Gln Val Asp Ser Ser Ser Leu Lys 535 540 545 AAC AAC ACC AAT GTT TCT GCA CTT CTC TGG GGC GGA TAC CCC GGC CAA 2618 Asn Asn Thr Asn Val Ser Ala Leu Leu Trp Gly Gly Tyr Pro Gly Gln 550 555 560 TCT GGC GGC TTC GCT TTG CGG GAT ATC ATC ACG GGG AAG AAG AAC CCC 2666 Ser Gly Gly Phe Ala Leu Arg Asp Ile Ile Thr Gly Lys Lys Asn Pro 565 570 575 GCG GGT AGA CTA GTC ACG ACG CAG TAC CCT GCC AGC TAC GCG GAG GAG 2714 Ala Gly Arg Leu Val Thr Thr Gln Tyr Pro Ala Ser Tyr Ala Glu Glu 580 585 590 TTC CCG GCG ACA GAT ATG AAC CTT CGT CCT GAG GGT GAT AAC CCT GGT 2762 Phe Pro Ala Thr Asp Met Asn Leu Arg Pro Glu Gly Asp Asn Pro Gly 595 600 605 610 CAG ACG TAT AAA TGG TAC ACC GGC GAA GCC GTG TAC GAG TTC GGC CAC 2810 Gln Thr Tyr Lys Trp Tyr Thr Gly Glu Ala Val Tyr Glu Phe Gly His 615 620 625 GGG TTA TTC TAC ACG ACC TTC GCG GAA TCC TCC AGC AAT ACC ACT ACA 2858 Gly Leu Phe Tyr Thr Thr Phe Ala Glu Ser Ser Ser Asn Thr Thr Thr 630 635 640 AAG GAA GTT AAG CTC AAC ATC CAG GAC ATT CTT TCC CAG ACA CAC GAA 2906 Lys Glu Val Lys Leu Asn Ile Gln Asp Ile Leu Ser Gln Thr His Glu 645 650 655 GAC CTG GCG TCG ATT ACC CAG CTC CCT GTG CTG AAC TTC ACC GCC AAT 2954 Asp Leu Ala Ser Ile Thr Gln Leu Pro Val Leu Asn Phe Thr Ala Asn 660 665 670 ATC AGG AAC ACT GGA AAG CTG GAA TCG GAT TAC ACC GCT ATG GTA TTC 3002 Ile Arg Asn Thr Gly Lys Leu Glu Ser Asp Tyr Thr Ala Met Val Phe 675 680 685 690 GCC AAT ACC TCT GAT GCC GGG CCG GCG CCG TAT CCC AAG AAG TGG CTG 3050 Ala Asn Thr Ser Asp Ala Gly Pro Ala Pro Tyr Pro Lys Lys Trp Leu 695 700 705 GTC GGG TGG GAT CGG CTT GGG GAG GTG AAG GTC GGG GAG ACG AGG GAG 3098 Val Gly Trp Asp Arg Leu Gly Glu Val Lys Val Gly Glu Thr Arg Glu 710 715 720 TTG AGG GTC CCC GTT GAG GTG GGG AGC TTT GCG AGG GTG AAT GAG GAT 3146 Leu Arg Val Pro Val Glu Val Gly Ser Phe Ala Arg Val Asn Glu Asp 725 730 735 GGC GAT TGG GTG GTG TTT CCG GGA ACG TTT GAG TTG GCG TTG AAT TTG 3194 Gly Asp Trp Val Val Phe Pro Gly Thr Phe Glu Leu Ala Leu Asn Leu 740 745 750 GAG AGG AAG GTT CGG GTG AAG GTT GTT CTT GAG GGT GAG GAG GAA GTC 3242 Glu Arg Lys Val Arg Val Lys Val Val Leu Glu Gly Glu Glu Glu Val 755 760 765 770 GTG CTG AAG TGG CCG GGG AAG GAG TAGAAAATAC TATTCTGTTG ATGGCTCTAG 3296 Val Leu Lys Trp Pro Gly Lys Glu 775 GGGATGAGAG TCAGCCTATT ACTGGATATG CATAGTGGTG ATACGATGTA TATAGCTCTA 3356 TGAAGTAATT AGTTCAAGTG GGAATACCCC TTTCACACAT ATAGTATGCT GTTATTCCGA 3416 AATAGGGATC ATTTCTGATT AATAGTAGCG GTAGCGATGG TCACACACGA CTTAATGTTC 3476 CCCATTGTAC CGGAAGTAAC AATTCCAGTG ACCTCTTAGA AGAAAGACAG CAAGAAAAAG 3536 TAAGAAAGGG AAATTGATCA AAAAATAAGG CCATCTACAG CCTATTCACA TTTAGCCGGA 3596 TCTGCAATAC AGCTACAGAA ATAAAGTTTG TTAGGCTGCT TGCTAGCATA GCTCCTACTA 3656 TACTAAACCA ACACAATGGG ACAATACCCC AATTAACCAG CCCTCACTCA ACACAAGTGA 3716 ATCCTACCGA CAACATGCAT AAACCACTGC TTCCCCACCC AGCACCCTTC TTCACGATCA 3776 GATCACGGAG AATTACCAAC TACTCTTCGC ATAAAACGTA AACAACGGCC TCGGGCCAGG 3836 ATCCGTCCGA CTCAAAAGCA ACAAATCCCT CGTTCGCATA CTAGCCACAT GAACCTGTTG 3896 CTCCGAGACC TCCTCAACTG GGTCTTCAAA TGCCCAGAAG ACGCTTTCTT CTCGATATCC 3956 ATCGGATACT CGCTGGCCGC TTAGACATAT GAACGATGAG TCTCGTCTGC CAAAGGAAAC 4016 AACCGTGTTC CCGAATCCAG TGTCAAAGTC GTAGGTCTGG AATTTGAAAA GTGTTCGGGC 4076 GTTTCCTTGG AGGGTCGGGA GTGCGACTGC AG 4108 (2) INFORMATION FOR SEQ ID NO: 9: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 4173 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iii) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Aspergillus niger (B) STRAIN: CBS 120.49 (C) INDIVIDUAL ISOLATE: N400 (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: join(948..1173, 1238..3495, 3550..3690) (C) IDENTIFICATION METHOD: experimental (D) OTHER INFORMATION: /function= “Transcriptional activator of xylanolytic genes” /product= “Binuclear Zn finger DNA binding protein” /gene= “xlnR” /standard_name= “XYL R” (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 948..1173 (ix) FEATURE: (A) NAME/KEY: intron (B) LOCATION: 1174..1237 (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 1238..3495 (ix) FEATURE: (A) NAME/KEY: intron (B) LOCATION: 3496..3549 (ix) FEATURE: (A) NAME/KEY: exon (B) LOCATION: 3550..3690 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 9: CCCGGGCTTG GTTGGTCTCC GTCTGGCTTC CCCGCCTTTT TCCCCTGCAA TTCTGCATCC 60 CCAATCCTTC TTTTTTCTTT GCCTCGCCAG GCTGTGTCTT TTTTCCCCCT CCCCCTCCTC 120 CCTCGTCAGC TTCTCTTCGA CAGCATGCGT GAGGGTCTGC TACCAACTAC AATCCTTGTT 180 CTCACTGTCT GATGGTCTGA CCCGACCGTG GTGTCTGTGG TGTGTGTGTG AGAGAGAAAG 240 GAAAGCTAGT CAGTCCAGTC ACTCTTTCTC GTGGGTTCTT CACCTTCCCC GGACCTGCCC 300 TCCGACACTA AAAAGCCACT TCCCCCCAAC TGGTTAGTTG CTGCTAGTCT CCTTAGTTCA 360 TGGTCGGCCT TGTCGCTTCT CCGGCTGACA TTCTCCTCTT CTGCTGCCTT CTAGGTCCCT 420 GTTTTTTAGT CCCTGTTTTA GTTGCCCCGC AGACTGAATC GGCAATGCCG TGGAGTTGAT 480 CGTTCCGTGG TTTCCTTGCG ACCGCTCCTC TGCTTCATCA TCTTTTTCCT CCTGCCCTCC 540 TGGTCTTGAA TCGCCTGGCC CTCGTCTAGG ATCTGTTGCG CCAGTGTCGC CTTAATCTCC 600 TTTCCCGCTA GCGTAGTGCC CTTTCACGCT TGGGGCCTTA CGGCCCTTCC ATTCGCCAGC 660 GGTCTGAATA CCTCACTTTC CCCCCCAACG ACCGGGGTCT TCATGACCCG CTGGGGTGAT 720 TGTTCCGCCC GGTGAGGATG TCAACCCCCT CGATTCCTCA ATTCACCAGT CCTTTCTCTC 780 CCTTCTCTTC CGGATCGCAC TCGACTGGCA TGGCGCCGTC TCAGACTGTC GGGTTGGATA 840 CGCTCGCCGA GGGCTCGCAG TACGTCCTGG AACAATTGCA GCTGTCGCGA GACGCTGCGG 900 GAACCGGTGC CGGCGATGGC GCGACCTCCA CTTCCTTGCG AAATTCC ATG TCG CAT 956 Met Ser His 1 ACG AAG GAT CAA CCA CCC TTT GAT AAT GAG AAG AAC CAG AGC ACT GGC 1004 Thr Lys Asp Gln Pro Pro Phe Asp Asn Glu Lys Asn Gln Ser Thr Gly 5 10 15 TCG GGT TTT AGG GAC GCT CTG CAA AGA GAT CCC CTC GTG GAG GCT CGC 1052 Ser Gly Phe Arg Asp Ala Leu Gln Arg Asp Pro Leu Val Glu Ala Arg 20 25 30 35 TCT GCC GTC CGC AAA ACC TCG TCT TCA GCT CCG GTT CGC CGC CGA ATC 1100 Ser Ala Val Arg Lys Thr Ser Ser Ser Ala Pro Val Arg Arg Arg Ile 40 45 50 AGC CGT GCG TGT GAC CAG TGT AAC CAA CTC CGA ACG AAA TGC GAC GGG 1148 Ser Arg Ala Cys Asp Gln Cys Asn Gln Leu Arg Thr Lys Cys Asp Gly 55 60 65 CAG CAT CCG TGC GCT CAT TGC ATT G GTAGGCTTCC GCTCTTTCTC 1193 Gln His Pro Cys Ala His Cys Ile 70 75 CGATGCCGGC GATGAGGCGG ACGCTTGACT GACCTGTTCT GTAG AA TTC GGA CTG 1248 Glu Phe Gly Leu ACC TGC GAG TAT GCG CGA GAA CGC AAG AAG CGT GGA AAA GCG TCG AAG 1296 Thr Cys Glu Tyr Ala Arg Glu Arg Lys Lys Arg Gly Lys Ala Ser Lys 80 85 90 95 AAG GAT CTG GCG GCG GCA GCT GCG GCG GCT ACC CAA GGG TCG AAT GGT 1344 Lys Asp Leu Ala Ala Ala Ala Ala Ala Ala Thr Gln Gly Ser Asn Gly 100 105 110 CAT TCC GGG CAG GCC AAC GCG TCG CTA ATG GGC GAG CGA ACG TCG GAA 1392 His Ser Gly Gln Ala Asn Ala Ser Leu Met Gly Glu Arg Thr Ser Glu 115 120 125 GAC AGC CGG CCA GGA CAA GAC GTG AAC GGC ACA TAC GAC TCG GCT TTT 1440 Asp Ser Arg Pro Gly Gln Asp Val Asn Gly Thr Tyr Asp Ser Ala Phe 130 135 140 GAG AGC CAC CAT CTT AGC TCG CAG CCA TCG CAT ATG CAG CAT GCA AGC 1488 Glu Ser His His Leu Ser Ser Gln Pro Ser His Met Gln His Ala Ser 145 150 155 ACT GCA GGG ATA TCC GGC CTG CAC GAG TCT CAG ACG GCA CCG TCG CAT 1536 Thr Ala Gly Ile Ser Gly Leu His Glu Ser Gln Thr Ala Pro Ser His 160 165 170 175 TCG CAA TCA TCG CTA GGA ACG ACT ATC GAT GCG ATG CAT TTG AAT CAT 1584 Ser Gln Ser Ser Leu Gly Thr Thr Ile Asp Ala Met His Leu Asn His 180 185 190 TTC AAC ACG ATG AAC GAT TCC GGT CGC CCG GCA ATG TCC ATA TCC GAT 1632 Phe Asn Thr Met Asn Asp Ser Gly Arg Pro Ala Met Ser Ile Ser Asp 195 200 205 CTG CGT TCG CTA CCC CCG TCC GTC TTA CCA CCG CAA GGA CTA AGC TCC 1680 Leu Arg Ser Leu Pro Pro Ser Val Leu Pro Pro Gln Gly Leu Ser Ser 210 215 220 GGG TAC AAC GCG AGC GCC TTC GCT TTG GTG AAC CCG CAA GAG CCG GGC 1728 Gly Tyr Asn Ala Ser Ala Phe Ala Leu Val Asn Pro Gln Glu Pro Gly 225 230 235 TCA CCA GCT AAC CAG TTT CGC TTG GGA AGC TCA GCG GAA AAC CCA ACC 1776 Ser Pro Ala Asn Gln Phe Arg Leu Gly Ser Ser Ala Glu Asn Pro Thr 240 245 250 255 GCA CCG TTT CTT GGT CTC TCG CCT CCA GGA CAG TCG CCT GGA TGG CTC 1824 Ala Pro Phe Leu Gly Leu Ser Pro Pro Gly Gln Ser Pro Gly Trp Leu 260 265 270 CCT CTT CCC TCG CCA TCT CCT GCC AAC TTT CCT TCT TTC AGC TTG CAT 1872 Pro Leu Pro Ser Pro Ser Pro Ala Asn Phe Pro Ser Phe Ser Leu His 275 280 285 CCG TTT TCC AGC ACT TTA CGA TAC CCT GTT TTG CAG CCG GTC CTG CCT 1920 Pro Phe Ser Ser Thr Leu Arg Tyr Pro Val Leu Gln Pro Val Leu Pro 290 295 300 CAC ATC GCC TCC ATT ATT CCG CAG TCG CTA GCG TGT GAC CTT CTG GAT 1968 His Ile Ala Ser Ile Ile Pro Gln Ser Leu Ala Cys Asp Leu Leu Asp 305 310 315 GTT TAC TTC ACT AGT TCC TCT TCG TCC CAC CTG TCT CCC TTG TCC CCA 2016 Val Tyr Phe Thr Ser Ser Ser Ser Ser His Leu Ser Pro Leu Ser Pro 320 325 330 335 TAC GTG GTG GGC TAC ATC TTC CGC AAG CAG TCT TTC CTT CAC CCG ACA 2064 Tyr Val Val Gly Tyr Ile Phe Arg Lys Gln Ser Phe Leu His Pro Thr 340 345 350 AAA CCC CGA ATA TGC AGC CCC GGT CTC CTG GCG AGT ATG CTC TGG GTA 2112 Lys Pro Arg Ile Cys Ser Pro Gly Leu Leu Ala Ser Met Leu Trp Val 355 360 365 GCC GCA CAA ACG AGT GAA GCT GCG TTT CTG ACA TCG CCG CCC TCG GCT 2160 Ala Ala Gln Thr Ser Glu Ala Ala Phe Leu Thr Ser Pro Pro Ser Ala 370 375 380 CGG GGG CGT GTA TGC CAG AAA CTG CTA GAA CTG ACC ATT GGT TTG CTC 2208 Arg Gly Arg Val Cys Gln Lys Leu Leu Glu Leu Thr Ile Gly Leu Leu 385 390 395 CGA CCG TTG GTC CAT GGT CCT GCT ACC GGA GAA GCG TCG CCC AAC TAT 2256 Arg Pro Leu Val His Gly Pro Ala Thr Gly Glu Ala Ser Pro Asn Tyr 400 405 410 415 GCG GCG AAT ATG GTC ATC AAT GGC GTC GCT CTG GGC GGA TTT GGG GTC 2304 Ala Ala Asn Met Val Ile Asn Gly Val Ala Leu Gly Gly Phe Gly Val 420 425 430 TCC ATG GAT CAG CTG GGC GCG CAA AGT AGC GCC ACC GGC GCC GTG GAT 2352 Ser Met Asp Gln Leu Gly Ala Gln Ser Ser Ala Thr Gly Ala Val Asp 435 440 445 GAT GTA GCA ACT TAT GTG CAT CTT GCG ACA GTA GTA TCC GCC AGC GAG 2400 Asp Val Ala Thr Tyr Val His Leu Ala Thr Val Val Ser Ala Ser Glu 450 455 460 TAC AAG GCG GCC AGC ATG CGC TGG TGG ACT GCG GCG TGG TCT CTA GCG 2448 Tyr Lys Ala Ala Ser Met Arg Trp Trp Thr Ala Ala Trp Ser Leu Ala 465 470 475 CGT GAG CTG AAG CTA GGC CGT GAG CTG CCA CCC AAT GTT TCC CAC GCA 2496 Arg Glu Leu Lys Leu Gly Arg Glu Leu Pro Pro Asn Val Ser His Ala 480 485 490 495 CGG CAA GAT GGA GAG CGA GAT GGG GAT GGC GAG GCG GAC AAA CGA CAT 2544 Arg Gln Asp Gly Glu Arg Asp Gly Asp Gly Glu Ala Asp Lys Arg His 500 505 510 CCT CCG ACC CTC ATC ACG TCA CTG GGT CAT GGA TCG GGA AGC TCC GGC 2592 Pro Pro Thr Leu Ile Thr Ser Leu Gly His Gly Ser Gly Ser Ser Gly 515 520 525 ATT AAT GTC ACC GAA GAG GAG CGT GAG GAG CGT CGA CGC CTA TGG TGG 2640 Ile Asn Val Thr Glu Glu Glu Arg Glu Glu Arg Arg Arg Leu Trp Trp 530 535 540 CTC TTA TAT GCG ACC GAT CGG CAC CTG GCG CTG TGC TAC AAC CGG CCC 2688 Leu Leu Tyr Ala Thr Asp Arg His Leu Ala Leu Cys Tyr Asn Arg Pro 545 550 555 CTC ACG CTG CTG GAC AAG GAA TGT GGC GGG CTG CTG CAG CCG ATG AAC 2736 Leu Thr Leu Leu Asp Lys Glu Cys Gly Gly Leu Leu Gln Pro Met Asn 560 565 570 575 GAT GAT CTG TGG CAG GTC GGC GAC TTT GCA GCG GCT GCC TAC CGC CAG 2784 Asp Asp Leu Trp Gln Val Gly Asp Phe Ala Ala Ala Ala Tyr Arg Gln 580 585 590 GTC GGA CCG CCC GTC GAG TGT ACG GGT CAC AGC ATG TAT GGA TAC TTT 2832 Val Gly Pro Pro Val Glu Cys Thr Gly His Ser Met Tyr Gly Tyr Phe 595 600 605 CTA CCG CTG ATG ACG ATT CTT GGA GGG ATC GTC GAT CTG CAC CAC GCT 2880 Leu Pro Leu Met Thr Ile Leu Gly Gly Ile Val Asp Leu His His Ala 610 615 620 GAG AAT CAT CCG CGC TTT GGC CTG GCG TTC CGC AAT AGC CCG GAG TGG 2928 Glu Asn His Pro Arg Phe Gly Leu Ala Phe Arg Asn Ser Pro Glu Trp 625 630 635 GAG CGT CAG GTA CTG GAC GTT ACG CGG CAG CTG GAC ACA TAT GGG CGC 2976 Glu Arg Gln Val Leu Asp Val Thr Arg Gln Leu Asp Thr Tyr Gly Arg 640 645 650 655 AGC TTG AAG GAA TTC GAG GCC CGC TAC ACC AGC AAC TTG ACT CTG GGG 3024 Ser Leu Lys Glu Phe Glu Ala Arg Tyr Thr Ser Asn Leu Thr Leu Gly 660 665 670 GCT ACG GAT AAC GAG CCT GTC GTC GAA GGT GCC CAC TTG GAT CAC ACG 3072 Ala Thr Asp Asn Glu Pro Val Val Glu Gly Ala His Leu Asp His Thr 675 680 685 AGT CCT TCG GGG CGC TCC AGC AGC ACC GTG GGA TCG CGG GTG AGC GAG 3120 Ser Pro Ser Gly Arg Ser Ser Ser Thr Val Gly Ser Arg Val Ser Glu 690 695 700 TCC ATC GTC CAC ACG AGG ATG GTG GTC GCC TAC GGG ACG CAT ATC ATG 3168 Ser Ile Val His Thr Arg Met Val Val Ala Tyr Gly Thr His Ile Met 705 710 715 CAC GTC CTG CAT ATT TTG CTC GCG GGA AAA TGG GAC CCG GTG AAT CTG 3216 His Val Leu His Ile Leu Leu Ala Gly Lys Trp Asp Pro Val Asn Leu 720 725 730 735 TTG GAA GAT CAT GAT CTG TGG ATC TCC TCG GAG TCG TTT GTC TCG GCC 3264 Leu Glu Asp His Asp Leu Trp Ile Ser Ser Glu Ser Phe Val Ser Ala 740 745 750 ATG AGC CAT GCG GTC GGT GCC GCA GAA GCA GCG GCA GAA ATC TTG GAG 3312 Met Ser His Ala Val Gly Ala Ala Glu Ala Ala Ala Glu Ile Leu Glu 755 760 765 TAC GAC CCG GAT CTC AGC TTC ATG CCG TTC TTC TTC GGG ATT TAC CTA 3360 Tyr Asp Pro Asp Leu Ser Phe Met Pro Phe Phe Phe Gly Ile Tyr Leu 770 775 780 CTA CAG GGC AGT TTC TTG CTG CTA CTG GCG GCG GAC AAG TTG CAG GGC 3408 Leu Gln Gly Ser Phe Leu Leu Leu Leu Ala Ala Asp Lys Leu Gln Gly 785 790 795 GAT GCC AGT CCC AGT GTC GTG CGG GCA TGC GAG ACG ATC GTG CGG GCG 3456 Asp Ala Ser Pro Ser Val Val Arg Ala Cys Glu Thr Ile Val Arg Ala 800 805 810 815 CAT GAA GCG TGC GTC GTG ACC TTG AAC ACG GAG TAC CAG GTAGGTTTTC 3505 His Glu Ala Cys Val Val Thr Leu Asn Thr Glu Tyr Gln 820 825 TTGTTTCTCT CCCTAGCTTG GCAATAGTAG CTAACACAAT GTAG AGG ACA TTC CGC 3561 Arg Thr Phe Arg 830 AAG GTC ATG CGA TCG GCG CTG GCA CAG GTT CGA GGA CGC ATC CCA GAG 3609 Lys Val Met Arg Ser Ala Leu Ala Gln Val Arg Gly Arg Ile Pro Glu 835 840 845 GAC TTT GGG GAG CAG CAG CAG CGC CGA CGC GAA GTG CTT GCG CTA TAC 3657 Asp Phe Gly Glu Gln Gln Gln Arg Arg Arg Glu Val Leu Ala Leu Tyr 850 855 860 CGC TGG AGC GGC GAT GGC AGT GGG CTG GCA CTG TAGTTTTGCA GTAACACGGC 3710 Arg Trp Ser Gly Asp Gly Ser Gly Leu Ala Leu 865 870 875 TGATGATGAG ATGCGATTTA TGGCGGTGCA TTGACCGGTC AATGGCTTCT TACATTCTGA 3770 TTTGATACTA CTTTTGGATT CGCTATTTCA CTCCGGGCTT ATGCTGGCTT CATTGTCAAG 3830 AGGGGTGGCA TGGCGAATGG AAATATGCTT ACTTCGTGTT GATACGGATT CGTACATATA 3890 CTTTGGTGAT ATATGTGGAT ATTTGTGGCA TGTACACTAT GCGTGATCTT TGGACATGAT 3950 ACTTTGATAC CAGGTCAATC TAATTGCGTT CTTTTCATTT GTTGCGCAAC AGCCGAGGTA 4010 TGACGCCATG GCTGAGATAA GCTGCCGATA AGCATTCGCA TTCCATCCTC CATCGAAGCA 4070 CCAAAATCTT CTTCATATAA CCAATCCATC AATTCAACAT TCGTAATGAC AATAGTATAA 4130 TCCCCAAAAT GCCCTCCCTA TTACACTCCC TCCGCACTTC CCC 4173 (2) INFORMATION FOR SEQ ID NO: 10: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 30 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 10: CACAATGCAT CGTATAAGTA ACCTCGTTCG 30 

What is claimed is:
 1. A method for preparing and selecting a mutant strain of a microorganism, wherein said mutant strain possesses a mutation that enhances a predetermined part of metabolism in comparison to a strain of said microorganisms not possessing said mutation, said method comprising the following steps: (a) introducing into a microorganism a nucleic acid cassette comprising: (i) a nucleic acid sequence encoding a bidirectional marker; (ii) a basic transcriptional unit operatively linked to the nucleic acid sequence encoding the bidirectional marker; and (iii) an inducible enhancer or activator sequence linked to the basic transcriptional unit in such a manner that upon induction of said inducible enhancer or activator sequence the bidirectional marker is expressed, said inducible enhancer or activator sequence being an inducible enhancer or activator sequence of a gene associated with metabolic activity, wherein said microorganism does not exhibit the phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette into said microorganism; (b) culturing the microorganism resulting from step (a) under conditions wherein the inducible enhancer or activator sequence of the nucleic acid cassette is active, and under conditions wherein the bidirectional marker is expressed; (c) selecting a transformant that exhibits the phenotype corresponding to expression of the bidirectional marker gene under the culturing conditions of step (b); (d) subjecting the transformant selected in step (c) to mutagenesis; (e) culturing the mutagenized transformant of step (d) under conditions acceptable for a strain with a phenotype corresponding to expression of the bidirectional marker and under conditions that in a non-mutated transformant of step (c) result in non-expression of the bidirectional marker, and in the presence of a metabolisable substrate for the predetermined part of metabolism; and (f) selecting a strain resulting from the culturing step (e) that exhibits a phenotype corresponding to expression of the bidirectional marker gene under selection conditions that for a non-mutated transformant of step (c) result in non-expression of the bidirectional marker.
 2. The method according to claim 1, wherein the inducible enhancer or activator sequence of the nucleic acid cassette is the Upstream Activating Sequence (UAS) of the gene xlnA; the predetermined part of metabolism is the xylanolytic part of carbon metabolism; the culturing step (b) occurs in the presence of an inducer of the UAS and in the absence of a repressor of the UAS, and a metabolisable source of carbon; and the culturing step (e) occurs in the presence of a repressor of the UAS and in the presence of a metabolisable source of carbon, and optionally also in the presence of an inducer of the UAS.
 3. A method for preparing and selecting a non recombinant mutant strain of a microorganism, wherein said mutant strain possesses a mutation that enhances a predetermined part of metabolism in comparison to a strain of said microorganism not possessing said mutation, said method comprising carrying out the steps of the method according to claim 1 followed by crossing out of the nucleic acid of the introduced nucleic acid cassette, thereby preparing and selecting a non recombinant mutant.
 4. The method according to claim 1, wherein prior to introduction of the nucleic acid cassette, the microorganism comprises nucleic acid corresponding at least in part to nucleic acid sequence encoding the bidirectional marker, said correspondence being to a degree sufficient to allow homologous recombination between the nucleic acid sequence encoding the bidirectional marker present in the microorganism and the nucleic acid sequence of the bidirectional marker in the nucleic acid cassette.
 5. The method according to claim 2, wherein the bidirectional marker of the nucleic acid cassette is pyrA; the microorganism does not exhibit a pyrA+ phenotype, associated with expression of the bidirectional marker, prior to introduction of the nucleic acid cassette into the microorganism; the culturing step (b) occurs in the presence of an inducer of the enhancer or activator and the absence of a repressor of the enhancer or activator, and under conditions wherein the bidirectional marker is expressed; the culturing step (e) occurs in the absence of an inducer of the enhancer or activator or in the presence of a repressor of the enhancer or activator, and in the presence of a metabolisable substrate for the predetermined part of metabolism; and the selection step (f) occurs in the absence of an inducer of the enhancer or activator, or the presence of a repressor of the enhancer or activator.
 6. The method according to claim 2, wherein the bidirectional marker of the nucleic acid cassette is pyrA; the microorganism does not exhibit a pyrA+ phenotype, associated with expression of the bidirectional marker, prior to introduction of the nucleic acid cassette into the microorganism; the culturing step (b) occurs in the presence of an inducer of the UAS and in the absence of a repressor of the UAS, and under conditions wherein the bidirectional marker is expressed; the culturing step (e) occurs in the absence of an inducer of the UAS or in the presence of a repressor of the UAS, and in the presence of a metabolisable source of carbon; and the selection step (f) occurs in the absence of an inducer of the UAS or the presence of a repressor of the UAS.
 7. The method according to claim 6, wherein the inducer of the UAS is xylose or xylan.
 8. The method according to claim 6, wherein the repressor of the UAS is glucose.
 9. A method of preparing and selecting a mutant strain of a microorganism, where said mutant strain possesses a mutation that reduces or inhibits a predetermined part of metabolism in comparison to a strain of said microorganism not possessing said mutation, said method comprising the following steps: (a) introducing into a microorganism a nucleic acid cassette comprising: (i) a nucleic acid sequence encoding a bidirectional marker; (ii) a basic transcriptional unit operatively linked to the nucleic acid sequence encoding the bidirectional marker; and (iii) an inducible enhancer or activator sequence linked to the basic transcriptional unit in such a manner that upon induction of said inducible enhancer or activator sequence the bidirectional marker is expressed, said inducible enhancer or activator sequence being an inducible enhancer or activator sequence of a gene associated with metabolic activity, wherein said microorganism does not exhibit the phenotype associated with expression of the bidirectional marker prior to introduction of the nucleic acid cassette into said microorganism and wherein said microorganism does exhibit activity of a type characterizing the predetermined part of metabolism to be reduced or inhibited; (b) culturing the microorganism resulting from step (a) under conditions wherein the inducible enhancer or activator sequence of the nucleic acid cassette is active, and wherein non expression of the bidirectional marker will result in growth and detection of the microorganism resulting from step (a), and wherein expression of the bidirectional marker will be lethal or strongly growth inhibiting; (c) selecting a transformant that exhibits the phenotype corresponding to expression of the bidirectional marker gene under the culturing conditions of step (b); (d) subjecting the transformant selected in step (c) to mutagenesis: (e) culturing the mutagenized transformant of step (d) under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the bidirectional marker and in the presence of a metabolisable substrate and under conditions that allow detection of reduced or inhibited activity of the predetermined part of metabolism in comparison to both a non mutated microorganism resulting from step (a) and a non mutated microorganism also not transfected with the nucleic acid cassette; and (f) selecting a strain resulting from the culturing step (e) that exhibits a phenotype corresponding to reduced or inhibited activity of the predetermined part of metabolism under selection conditions that allow detection of reduced or inhibited activity of the predetermined part of metabolism, in comparison to both a non mutated microorganism resulting from step (a) and a non mutated microorganism also not transfected with the nucleic acid cassette, said conditions being a reduced zone of clearing upon growth on a substrate which serves as a substrate for the part of metabolism for which activity is to be reduced or inhibited.
 10. The method according to claim 9, wherein the inducible enhancer or activator sequence of the nucleic acid cassette is the Upstream Activating Sequence (UAS) of the gene xlnA; the predetermined part of metabolism is the xylanolytic part of carbon metabolism; the culturing step (b) occurs in the absence of a repressor of the UAS, in the presence of a metabolisable source of carbon and also in the presence of an inducer of the UAS; the culturing step (e) occurs (i) under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the bidirectional marker, and under conditions that are unacceptable for growth and detection of a strain with a phenotype corresponding to the expression of the bidirectional marker, said conditions comprising culturing in the presence of uridine and fluoro-orotic acid, and (ii) under conditions that in a transformant selected in step (c) result in activity of the predetermined part of carbon metabolism, said conditions comprising culturing in the presence of an inducer of the UAS and a metabolisable carbon source and the absence of a repressor of the UAS; and the selection step (f) occurs under selection conditions that allow detection of reduced or inhibited activity of the predetermined part of carbon metabolism in comparison to both a non mutated microorganism resulting from step (a) and a non mutated microorganism also not transfected with the nucleic acid cassette, said conditions being a reduced zone of clearing upon growth on xylan.
 11. A method for preparing and selecting a non recombinant mutant strain of a microorganism, wherein said mutant strain possesses a mutation that inhibits a predetermined part of metabolism in comparison to a strain of said microorganism not possessing said mutation, said method comprising carrying out the steps of the method according to claim 9 followed by crossing out of the nucleic acid of the introduced nucleic acid cassette, thereby preparing and selecting a non recombinant mutant.
 12. A method for determining the identity and nucleic acid sequence of an activating regulator of an inducible enhancer or activator sequence, said method comprising the steps of: (a) performing a complementation test wherein a microorganism obtained according to claim 9 is transformed with parts of genomic DNA of the non mutated, non-transformed microorganism used in step (a) of claim 9; (b) selecting an activator-positive transformant as detected by expression of the bidirectional marker; and (c) comparing nucleic acid from the activator-positive transformant with nucleic acid of the mutant obtained in the method of claim 9 to isolate and identify nucleic acid present in the activator-positive transformant and mutated in the mutant obtained in the method of claim
 9. 13. The method according to claim 10, wherein the bidirectional marker of the nucleic acid cassette is pyrA; the microorganism does not exhibit a pyrA+ phenotype, associated with expression of the bidirectional marker, prior to introduction of the nucleic acid cassette into the microorganism; the culturing step (b) occurs in the presence of an inducer of the enhancer or activator and in the absence of a repressor of the enhancer or activator, and under conditions wherein the bidirectional marker pyrA is expressed; and the culturing step (e) occurs under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the directional marker, and under conditions that are unacceptable for growth and detection of a strain with a pyrA phenotype, said phenotype corresponding to expression of the directional marker, such conditions comprising the presence of uridine and fluoro-orotic acid.
 14. The method according to claim 10, wherein the bidirectional marker of the nucleic acid cassette is pyrA; the microorganism does not exhibit a pyrA+ phenotype, associated with expression of the bidirectional marker, prior to introduction of the nucleic acid cassette into the microorganism; the culturing step (b) occurs in the presence of an inducer of the UAS and in the absence of a repressor of the UAS and under conditions wherein the bidirectional marker pyrA is expressed; and the culturing step (e) occurs under conditions acceptable for growth and detection of a strain with a phenotype corresponding to the non expression of the bidirectional marker, and under conditions that are unacceptable for growth and detection of a strain with a pyrA phenotype, said phenotype corresponding to expression of the bidirectional marker, such conditions comprising the presence of uridine and fluoro-orotic acid.
 15. The method according to claim 10, wherein the inducer of the UAS is D-xylose, a non-repressing source of carbon in combination with xylan or a non-repressing source of carbon in combination with D-xylose.
 16. The method according to claim 14, wherein the inducer of the UAS is selected from the group consisting of D-xylose, xylan, a non-repressing source of carbon in combination with D-xylose, and a non-repressing source of carbon in combination with xylan.
 17. The method according to claim 14, wherein the repressor of the UAS is glucose. 